option B has some advantages over A, so as A has some advantages over B.
impact reduction
as mentioned in another answer frontal projection in the A case is smaller so the number of impacts can be lower than in case B. However if some significant impact happens, something sizeable, like a mass of let's say square meter of the hull, depending on speeds there may be different effects and in case of A it may go through the whole hull, axial-wise, while in B case it may affect only a section of the cylinder, still may be disastrous effects, but a portion of construction to survive can be bigger with the same impact.
But really depends on how protection and detection are done and other factors, if done right then generally A case is preferred.
acceleration
For acceleration cases, B may be better or may not, depends on tech and other factors, but general tendency holds - accelerating force can be applied to structural elements more evenly(if we have some line of nozzles on the side) while accelerating in A orientation it will have the most stresses at the bottom(engine/acceleration nozzle) which will put restrictions of accelerating rate for given length/mass of construction but lesser forces on top.
That difference can be mitigated by design and technological means, to some extent, but the B case is more freer in terms of length of construction.
Addressing that rotation pulsing regime of work of those engines - they do not have to rotate with the hull at all, so as it may be a perfectly fine mode of operation for some thermonuclear engine, or even be the only mode of operation it works - so depends on tech heavily, but generally is not a problem.
apparent gravity
it may be more convenient to have changes in "gravity" once some minutes than the constant inclination of that force. Constant inclination can affect tree growth, if acceleration time is long enough for that, and it may have some weird effects when there is no acceleration.
However, changing force periodically over a long period of time may have some unpredictable health effects, so with a slight advantage A wins here, but if the problem is known to have no bad side effects on humans convenience of straight-looking trees may win.
drag
B will have more drag aka deacceleration forces against the interstellar medium, that's a fundamental one.
All in all - A is preferable, most likely, but the difference isn't huge
Clarifications
it is an offtopic part of the answer, but it seems that my statements brought more misunderstanding even for the smart part of the community, than I have expected it to be.
Hence I kinda forced to put some context and perspective and dive a little bit into space habs design considerations. Not extensively, but it just a big topic by itself.
Structural stress by acceleration
- what I mention in the main body of the answer seems not apparent, so let try to clarify what's it meant
let's have some rudimentary picture drawing of A and B cases, left is B case, right is A case

in A case we have a typical rocket problem - internal pressure, thin walls, elongation in the direction of acceleration. The most compression force the structure experience is at the bottom where the weight created by acceleration is connected to the acceleration force created by the engine nozzle. or we can say it is a typical skyscraper problem - the bottom has to be stronger as it keeps the weight of everything above.
Case B has a different situation, it indeed is more dynamic, but is a separate question('ll address that too). The hull is loaded by stretching forces - it is internal atmosphere pressure, it is weight created by the rotation of that volume - all the soil, all the materials used so as humans try to escape and fly away, by ripping hull apart and one of the things holding it together is the tensile strength of the hull. But tearing apart I mean stretching hull construction until it breaks - direction and orientation of stress forces are important here.
engine working in the B case works against those created forces which would like to rip the hull apart. So in some sense(not so simple) but there is the reduction of those forces along the line of acceleration (on both sides of the hull next to the engine and on the opposite side). However, of course, it has a price and we have deformation and other changes including stress forces - in general, the situation gets less symmetrical.
here we have to touch 101 of interstellar with no FTL
- really guys, u have to put less magic in your questions, because u lose touch with reality, robbing yourself of the context and intricate details which as classics say is greater than a typical imagination.
Let's say we have a thermonuclear engine, exhaust 0.1c, target speed 0.9c. Applying rocket equation and ignoring relativistic effects which aren't that big here we get a picture:
- fuel to construction ratio is 22000:1 (deacceleration done by magic, not included)
- with 8.5m/ss we reach the target speed in about a year, so less than about 25% of our total travel time for the closest possible target.
if the target speed 0.1c(i know many like that number) then:
- fuel to construction ratio is 2.7:1 (deacceleration done by magic, not included)
- acceleration at 25% travel time - 0.1 m/ss, travel time close to 40 years to the closes target.
So accelerations of 0.01-1g cover pretty much every target speed which is practical.
And surprise surprise 0.01g is enough for all of those who do not see any practicality in interstellar speeds above 0.1c
Structural stress by acceleration, strikes back again
in case of A, and acceleration 0.01g the length of a cylinder is limited(if we take modern skyscraper as a somewhat lazy reference) by 100km, and it scales linearly, so 0.1g it is 10km, 1g it is around 1km
in the case of B, it is more tricky, but the first thing to notice that even 1g acceleration, forces from the engine comparable to the forces which already act on the hull structure and sort of (if we smear average it over the hull, which may or may not be the case by design, later about that) does not exceed them, and somewhat even counteracts them in some nonsymmetrical way.
So if your diameter of habitat is 20km as an example, u still have the ways to make all that work under 1g, in the respect to the structural integrity of the construction. As 1g is kinda too much for A and B. Sure where is the will are the ways, but it all depends on the maturity of technologies and we have the most basic situation here.
And the length of your 20-100km diameter habitat is not limited at all.
Second thing to notice is that 0.01g changes of apparent gravity barely even noticeable, it is like to drink a bottle of Kvas and increase your bodily water content by a 0.5-1L
yes, sure, 0.1g is more noticeable, but for closes targets, it does not reduce your travel time that much, if u keep the same target speed in goal, so it applicable not to all case
but what if u don't, 0.1g and >0.1c target speed
but is we stick to higher acceleration rates and willing to travel faster, mass ratio of fuel to construction:
- 0.1c, 2.7:1, with deacceleration 7.3:1
- 0.2c, 7.4:1, with deacceleration 55:1 <- close to your typical rocket
- 0.3c, 20.1:1, with deacceleration 404:1
- 0.4c, 54.6:1, with deacceleration 2980:1
here we use a fraction of light of speed as speed, but sure habitat as the space ship is good because u can use basically any speed even much lower than those, but then a difference between A and B is negligible or not existing, and one can use accelerations way bellow 0.01g.
So even with a 2.7(7.3) ratio, we have to think about fuel which we carry to propel the construction - where it is, how we carry it - is it inside of habitat or has it its own separate tank, how we combine all the stuff together, etc. And more so with other ratios, those questions have their solutions.
design, of a space habitat with the intention to accelerate it.
let's draw again:

- Great picture from me, as usual, I'm great, MIT license forever, we live and die for it, no pasaran!
So in some sense, it is your typical A case, in a sense engine and fuel block aren't rotating. There is a gap between it and the rotating space habitat hull we have to close somehow.
a thing to notice that the engine fuel tank block isn't rotating not for the reasons of engine management problems wear tear and difficulty to pulsate it which are no problems at all(and no I won't dive in it here, we already way off-topic, ask your own separate question about how thermonuclear engines work). reasons are mostly about fuel containment structure, which is an important question considering that even in a low case scenario it 7 times more than the whole habitat structure, with a slight acceleration of the structure in which fuel (H, D, T, He3) are stored can be very lightweight, basically non existing as we can have those things as ice form (beyond Neptune it is okay for hydrogen to be ice) or a liquid with low vapor pressure.
another thing to notice, engine placement isn't optimal, but again there are more reasons and more questions, and more design considerations - as an example we have ideas about great materials which work superiorly under tension(cnt) and no great materials that do the same with compression(first can be converted into a second, but there are nuances).
So we have a gap to close to accelerate the cylinder, to conduct accelerating force to it and there are ways to do so.
your typical maglev solution is easier to imagine on that scale and with that particular design - but its way too energy-hungry, tech-savvy, and all that
An easier solution would be some air cushion between the fuel block and cylinder, and gas pressure acts on the external shell of a cylinder, evenly distribute the force on it. The principle lays in direction of air bearings.
- again sure there are technical nuances to recapture that air as an obvious one and a lot more. They have their own solutions.
a bit more realistic design which considers few factors.
That oblivious gap problem emerges mostly because of reduction design, making it simpler than it actually may be.
if u still in the '70s and imagine cylindrical habitat like a plain rotating tin can - u do it wrong. it has to be a more complex structure, so as for benefits a different design may provide, so as a result of necessity to solve problems which are specific to such design.

one of the approaches is to have a multilayer structure, which advantages it may have:
- alleviate stress on the internal hull where humans are, or remove it almost completely. the internal structure is not stressed means, in the first place higher safety of inhabitants and lesser concerns about the degradation of the structure. it allows having a deeper soil, where u need it as an example(for tree and forests as an example).
- it also removes or eases constraints on the diameter of a structure so do take your 15km sky with you, which looks and feels like home.
Compensation is done by the pressure of gases which are in the volume where intermediate layers are placed. But we get friction of the hull and that surrounding air and if it gets supersonic it may be not the best thing to have. And for that, we have those intermediate layers, which also are shells. they are not necessarily massive or robust, something on a lower side, just to get the job done - which is to separate gas volumes and have certain, defined by design, differences in speeds of shells, keep it subsonic to whatever value is good. (layers are not needed, but it is a more advanced approach, or less)
How they don't rub each other or collide? yeah, imagine an airplane(this thing with wings) kind there are ways to keep those shells separate - more strictly it gets back to air- and hydrodynamic bearings.
Most of the structural load bears the last shell - external hull, which by the magic of that layered design can have zero(0) angular velocity. But at the same time, it is the most pressurized can and has to be the most strong out of all those layers. But what advantages it gives:
the part of the construction which holds things together, does not rotate and thus isn't affected by centrifugal effects, and its mass brings no additional requirements to the strength of the construction. Meaning as it does not rotate there are no additional forces we have to consider because of its mass.
or we can formulate it differently - there is no limit on the mass of the external shell. it can be as massive as a planet, or km's tick - and more massive a bigger internal volume habitat it can hold together. So it can be as tick as needed.
in a sense, it is the opposite situation and one closer to the reality than when we look at the guys who imagine them being able to burrow a hole in an asteroid and rotate it to make habitat from it and for some magical reason it does not fly apart by what is in essence greatly exceeding The Roche limit for the body. The shell does not rotate and it stays put.
another good thing about not rotating shell is the ability to put some loose layer on top of it, which won't fly away, but at the same time serves as a protective layer for all kinds of things, like laser rail gun projectiles ... uuups sorry, that's a different subject, like it protects against meteorites particles radiation, drunk rocket drivers, etc. And being in a loose state it does not mind that mich being bombarded periodically, maintenance is a low effort thing, etc.
and in the case of accelerating space hab, it is where your engines press and where(maybe) your fuel is and the shielding from enormous fusion reaction happening next to u, which effects dwarfs any other effect like space radiation or radiation from the collision with interstellar medium - if we talk about 0.1g as an example, so honestly the same with 0.01g I guess. This can be solved but then it requires a different approach to your engine attachment.
- I'm especially amused with the comments like at A case one end we will have shielding compartment etc - guys u are delusional, next to the end of cylinder unknown amounts of Kuskina mother happens per second, to propel the massive thing, and u think 10km apart from the place is a safe place? And if not, do u really think it much stable to accelerate the stick in A case(but that will be a separate matter). The way I drew it also isn't much better, but there is more flexibility, not necessarily by much, but still.
there are other advantages but enough about that for now? more space habitat question for wb, I guess.
Stability
Some mention stability and it is indeed an interesting question, and have to start from the very beginning - O'Neill cylinder is not stable, to begin with.
There 2 videos to illustrate:
Rotating Solid Bodies in Microgravity
Dancing T-handle in zero-g, HD
while all life happens at a pace habitat masses are moving inside of it, stresses change, minuscule bending happening, etc and even if it may be okay for a year or many years if we consider it over longer periods of time it is problem to be solved p reactive propulsion is one of the ways, multilayer structure another one out of many smart solutions we can come by.
To grasp instability of rotating rod it is not necessary to go to iss, it is a widely known problem in the machining of shafts, to which attention has to be paid.
So if someone imagines that pushing A case means more stability, it is not correct - a slight displacement on a different end for a structure that is rotating in one direction and being accelerated at the same time - is a first step for the whole construction to go haywire (it can compensate itself, but it depends on own frequencies and a lot of things) and if turning point conditions are missed, u can't do anything to save the situation - cutting down engine won't help, too late rotating forces already work on making it go out of control. u tilt engine - u do it even worse to the stick - the thing starting to wobble will be a best-case scenario.
A space habitat on the scale when it meaningful to call it a colony can't be considered a rigid body.
There is no other way but B (ed: not so fast boy)
Diving a little bit in some specifics of certain direction or specific design family of habitats - it is possible to see that for those there are no other ways but to be oriented in B orientation. And it does not matter how big the disadvantages or advantages of A are, it is the only way for that design to go - if we push the throttle a little.
it does not mean there aren't other designs and approaches which can't benefit from A, but I hope this clarifying section shows that there are designs that have their advantages to be built that way, on their own, fulfilling the space habitats function and which would prefer B case.
There is no other way but A (not so fast boy)
After extensive consultations with our space hab design engineer @John and him investigating papers on motion sickness (comment section for links and refs) it became apparent that even if B case may have some advantages from a structural perspective(so as problems), it has some disadvantages for human content of the space habitat. As a vector of apparent gravity will oscillate around a vertical axis, and it causing some unwanted consequences, like motion sickness, because the threshold is quite low, ~0.007 m/ss.
So people have to adapt, but it is not known which other consequences it may have to humans living 24.7.365 in such conditions. Have seen an infant living on a yacht in Atlantics, just recently on yt, seems doing fine enough, so as there are some historical tribes which live on floating means, so as there are people living half-year at sea, but still, it is a problem which has to be considered, especially on the scale millions or more of different people living in such conditions. 33% of children below age 12, are more sensitive to the problem, for lesser ages it can be as high as half of them. people adapt, but yeah the problem has to be investigated specifically before the B case is rated for humans.
- Good news for treemans - they do not have to have wind for their branches to grow healthy and strong, maybe.
So B case has problems as well.
There is no other way but A or B
The full circle here and we back at more moderate statement A and B have their pros and cons. And it is a matter of design decisions - which problems do you choose to negate and which you choose to live with. either way, no matter the choice there will be a price to pay for the decisions.