Not sure why you think flippers are impractical. The lower density of air means that thrust for a fin would be lower than in the water, but drag would also be lower. Also, you didn't say how fast the creature needs to move. Almost any fin at all would provide some thrust, so the only question is: what is the maximum thrust you could feasibly get? And that depends on how much mass you can allocate to muscle, the overall shape of the creature, and its surface roughness (to compute friction drag). If the creature isn't trying to compete with birds of prey in the speed department, then the frontal area and surface friction are probably not important, and you could get away with a large, thin, lazily waving tail fin, mostly made of chitin spines and a thin but tough membrane. You could probably get away with a medium-to-small fin also, at a compromise of performance.
If the creature moves slowly, then spherical is best. If it needs to move quickly, then making it long and skinny (or at least cylindrical) is best but compromises your lifting efficiency. Also, you probably can't put enough muscle and metabolism on it to make it "swim" quickly. Probably have to resign yourself to a very slow whale. It is likely to be unable to overcome most winds aloft, depending on its customary altitude. So, at best, it can maneuver within air currents but has little say in where it actually goes.
A bigger problem, I think, is: what does it eat? Surely it can't catch flying creatures unless it has a clever lure. Surely a floating gasbag simply isn't sturdy enough to survive claws and beaks. I like the idea of the floating greenhouse. This creature can possibly do something that terrestrial plants cannot: move above the treetop/cloud layer to get unobstructed sunlight. That should be the primary motivation for its airborne nature. It can get carbon and oxygen from CO2 in the air, and it could possibly "drink" clouds to get hydrogen/water. But it still needs to fix nitrogen, and get essential trace elements like phosphorus, sulfur, iron, and other minerals. For this, it could either be an herbivore, and munch on treetops to get these vitamins, or it could be a dirt scavenger.
Imagine having long tentacles that can drop down dozens of meters, scooping loose soil from along the ground. Being close to the ground would make it vulnerable to ground-based predators and birds of prey, so it would need to have some kind of defense against those. But it would spend most of its time as high as it could manage because it's too metabolically expensive for most birds to fly very high in the sky. Once it scoops up dirt, it rises aloft, and lets symbiotic mycorrhizal webs in the "buckets" of the tentacles do the hard work of extracting trace minerals from the dirt. Basically, the tentacles would be functionally equivalent to tree roots. Once the symbionts stop giving up nutrients, the skywhale dumps the dirt and grabs some more. Mountains are safer places for gathering dirt because of fewer predators, and less altitude change, but also have lower nutrient content because fewer plant/animal/bacterial species are churning through the soil. So their scavenging would depend on their current needs and the risks involved.
To protect against lighting strikes, the skywhales could form a metallic web across their skin, like the shell of an airliner. By offering a low-resistance conductive path for lightning, they should be able to avoid the worst effects of a strike. Iron may be too heavy to use as a conductor, so perhaps they could create carbon nanotubes or graphene as the Faraday cage, which can be constructed out of pure carbon. What would be especially interesting is to create a graphene supercapacitor and have them store some of the charges flowing across their skin to use defensively. This could, of course, also be used offensively. Imagine a region on their top surface which emits predator pheromones (whatever organic volatiles might attract birds, like even blood heme). A bird flies up and comes in for a landing, expecting an easy treat on the gasbag. But when it lands, the supercapacitor, charged up from flying through a nimbus cloud, discharges and electrocutes the unsuspecting bird just as it makes contact with the skin. Then a "mouth" opens up and swallows the victim into the digestive system. Of course, a carnivorous skywhale wouldn't need to eat dirt, since birds would presumably be able to provide all the trace nutrients. However, it might not be able to eat enough birds to meet all its metabolic needs, so symbiotic/intrinsic photosynthesis would still be valuable.
I think the most difficult problem is actually lift. A fish can change its buoyancy easily because gas has a much lower density than water. So a swim bladder is relatively efficient space-wise. A proportionally sized swim bladder in your skywhale wouldn't give much altitude change. So you probably need to squeeze the entire gasbag to descend, which would presumably cost a lot of energy. The amount of work required to descend all the way to the ground, using just volumetric compression (as opposed to releasing gas) is basically the same as a hiker climbing from the ground to its maximum altitude (the altitude at which the gasbag is fully inflated). Only, the climber weighs half a ton. More problematic than the work (which can be done slowly over a long time) is the amount of force required to squeeze the gasbag because this puts hard lower bounds on the amount of muscle mass needed. The higher the max altitude, the more force required to squeeze it to the ground. Getting above 1000m may be infeasible.
Alternatively, it could simply dump hydrogen to descend quickly, and refill once it gets to the ground or a low cloud layer. At the surface, it would probably need to hover over a decent water source to obtain sufficient hydrogen to ascend. Otherwise, it would need to scavenge water vapor from clouds. And separating hydrogen from oxygen or alkanes or carbohydrates is energetically expensive (although most expensive for oxygen and least for alkanes, I think...methane is probably the easiest H source), so it couldn't do this quickly or easily. It could take days or weeks to refill the gasbag. If it relies heavily on photosynthesis, then dipping below the cloud layer could prove fatal, and possibly strand it near the ground for a long time.
Anyway, those are some things to think about. Have fun!