So, done some more thinking, and have had these ideas:
1. If we replace the Terran vHP units with Ghosts (or one of the Ghost Heroes) and the Protoss vHP with, for example, the Dark Templar Hero (Not Zeratul, the unit they used for the DTs in Episodes 2 and 3) (or whatever, that was just an example), and re-arranged the building lists, then we might be able to put the Engineering Bay, Forge, or Evolution Chamber on the ships (possibly as a control system building?), so then the player might lose the ability to upgrade his vHP armor until rebuilt.
2. We might be able to use Valkyries and Corsairs: Set it so that if a Corsair player builds his Upgrade to Hero building, he turns into a Valk. Or visa-versa.
3. I think Overlords should be the only ones allowed to spawn non-Drone units and deploy them: It doesn't fit with the Mutalisk and it's derivatives, nor with the Queen. (BUT, we might do it that the Queen can create Broodlings? Morph an Overlord at the Hatchery, and it vanishes and you get two Broodlings at your location...)
4. Possible cool idea: Have the crew of the ship talk to you. (Of course, not on for Zerg players.) What I mean is, get quotes from various sci-fi shows/movies/games (Star Trek, Star Wars, Babylon 5, Andromeda, or even 'Craft) and play them at various times. (Like, the player looses his last armor building: Have Worf from The Next Generation say "Shields down!". If a Protoss player's Fleet Beacon dies, you can play something from Andromeda where Andromeda (the Ai) says that she's loosing control of the ship systems.) The Zerg ship can grunt in pain (Play various Zerg unit noises, especially death noises) when it gets hit.
EDIT: I was confused about this. It doesn't seem to make sense... Not insulting the idea in any way, I just tend to have trouble understanding things...
You start off as a guardian. Off to the side somewhere there you would have a drone that you could put on 3 different beacons - one that has a guardian hovering over it, one with devourer, and the last one with muta. If you have a Spire you can go on the one with the devourer on it. If you have a Greater Spire you can go on the one with the mutalisk on it. If you go to one, you become a vulnerable cacoon for a little while (like 10-15 seconds) and then you turn into the guy you chose. Each has its advantages - guardian and devourer do more damage than the muta tho they attack slower. So you can change your form at any time if you have the right building. If you don't have a spire and you are a devourer you turn back into a guardian. Same sort of thing if you are a muta. Other buildings would do terran and protoss like things.
And: *agrees with above*
None.