I think it would be great that even if not all the prior races show up in the game due to respect for the original story, there should be the option of using them in melee. Even the SC3 ships. Yup, even them. But not always.
My feeling is there should be a code Star Control Reboot (are we calling this SCPrime or something? I've seen some references on the forum) set of ships that's available for competitive multiplayer, balanced versus, etc. But there also should be an expanded section that brings back every ship already seen in SC games and maybe a few cameos or nods to other games.
It would be especially cool if in addition to the adventure mode there was a dynamic scenario mode where you could set up a little galaxy and battle through, recruit, etc all these races without it being a part of the lore - kind of a basic 4x strategic mode just to facilitate battles in a way that's more fun than just playing the PC with a fleet that you've set up.