Why would a sublight Alcubierre drive be more useful for braking than for propulsion?

To get to the point, ships in the setting I'm working on still use a conventional, albeit very advanced, form of rocket propulsion.

However interstellar ships also use a sublight Alcubierre drive which can't efficiently be used for travel by itself. Rather the main use of the warp bubbles is to aid the ship in maneuvering, shielding and braking.

Instead of flipping and burning in the direction of their destination, ships usually reorient their warp bubbles, creating a gravitational gradient in the opposite direction.

However an inconsistency I foresee with this idea, is that if warp bubbles are strong enough to decelerate the ship, then logically wouldn't they also be powerful enough to be used as propulsion by themselves?

How would I handwave this problem?

How the technology works precisely, doesn't entirely matter. The only thing that I care about is that I don't end up breaking the setting with easy RKKVs or perpetual motion machines.

Like you noted in the question, deceleration is acceleration. The only difference is your preferred frame of reference. With that said, to get what you're wanting the only solution I can see is invoking a preferred frame of reference for your warp drives.

When stationary against the preferred frame of reference, the warp drive is incapable of doing anything, like a ship stuck in still seas and still air. Only when the ship has velocity relative to the air can the ship slow or change direction.

Where does the preferred frame come from?

From your description it sounds like your ships do a lot of system-hopping. During transit they'll have large velocities relative to the central sun, so I suggest making the solar barycenter the preferred frame. Warp drives can grind to a halt relative to it, or slow as well as needed to match velocities with the destination, and then conventional rockets close the delta-v gap.

Why physically the barycenter? Maybe it has something to do with local space-time curvature that enforces the constraints on warp fields. If the warp drive doesn't experience the curvature gradient (isn't moving from highly-curved space into less-curved space, or vice versa) then it can't push or pull, like a heat engine can't push or pull if it doesn't have a temperature gradient to work with.

This probably means the best place to park a warp drive ship would be on highly elliptical orbits. The worst places would be circular orbits or Lagrange points, as the ship would need an initial rocket burn to get going.

It's not that they couldn't be used for acceleration, it's just that they require a lot of fuel. So, if they were used for acceleration the ship would have to accelerate the entire mass of fuel intended for acceleration and deceleration. Which would require much more fuel and time and make the ship K times larger and the whole flight X times longer.

Instead, for acceleration solar sails receive energy from home planet system via enormous lasers. When the ship eventually starts decelerating it has to rely on it's precious fuel reserves to feed the engines.

The ship doesn't actually carry everything needed to form the warp bubble. The equipment on the ship anchors one to the ship once formed, but forming one requires part of the structure to moving past the ship at a velocity comparable to what the ship wants to shed. Thus, the ship performs a high-speed flyby of a deep space "tollbooth" that provides the other half of the system needed to form the braking bubble. The resulting bubble's acceleration direction and total delta-v are fixed and determined by the flyby, so it is really only useful for braking relative to the tollbooth.

There's two ways you can go from here:

1. If the braking bubble immediately starts the deceleration, the tollbooth must either be placed at the target system or the ship must decelerate over the entire trip, effectively doubling the length of the trip. This makes it somewhat of a barrier against traveling outside the transportation network.
2. If the ship can "hold" the bubble and use it to decelerate on demand, the tollbooth can be used to generate it on the way out of the origin system. Then you can stop whenever you want, but you need to place a new tollbooth if you want to go somewhere else after stopping.

Perhaps the latter is a capability only special exploration ships have, most ships not wanting to take the risk of having to keep the bubble intact until it's needed for deceleration.