ST4 needed the ship for much of the movie but not for space battles of course. Without a ship there was no time travel nor any way to get the whales. They could have come up with some other kind of method but since the idea of using a ship was already established they didnt have to spend the time explaining how a different method would work. Certainly whatever method would have to make sure the whales were always in water. So its either a self-contained vehicle or time travel directly within the ocean.
As for Trek 2011, do some kind of battle in the beginning 15 minutes as a setup but thats it. Solve whatever plot complication without needing the ship except in a minimal way only.
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