GAFY - I'm pretty much torn down the middle about it, to the point where I'm tempted to do both >.<, I just figured I'd knock and the sky and listen to the sound.
The one texture sheet makes them convertable to other games, a plus, and if they change the basic engine out for one from another game it would be easier to convert your ships.
1 2048 x 2048 basically covers the same area, or more, as most models use anyways on 6-8 seperate sheets. it usually is 2 1024 x 1024, 1 1024 x 512 and 2-3 512 x 512 sheets.
so a 1 sheet approach has its advantages, as long as the PSD file is sectioned correctly and named right it can be done quite easily for change outs as well using groupings and the abilies to hide all or part of them. So use the one sheet either way and if you wish to go back and bake them, if you side against it, it will be easy to do. Guess you should put the two pics back up of the ship you had with both versions baked and non-baked and put it up to a vote. My vote is for which one takes you less time and effort, as that in the end is always the deciding factor.
so i guess I am a combo player in the vote, single sheet and which ever method takes the least effort and time, you can always go back to the other method with this approach.