The major issue that I see with this is what happens when the transport dies over land? Would the ship die? Would it be stuck? Take constant damage? Slide downhill?
The best suggestion I can think of for this would be slide down hill until it hits flat land or water taking damage until it stops. I think that maybe it should be able to fire but try to make the ships land so that they don't have full range of fire (can shoot off one side, but the only really close on the other because it's setting at an angle).
Transporting the carrier seems a bit much, but if it were allowed, I would suggest that spawning of drones be disabled in flight (carrier-napping possible).
I could see subs being transportable with the limitation of allied subs (enemy subs won't surface for transport).
Overall, I think it's a good solution for mixed maps as hovers are the only surface based unit that can currently traverse them. Puddle jumping would be a great way to allow recapture or reinforcement of a secondary water area and give new meaning to anti-air on the land between.
