I'd just like to throw in my two cents.
From what I can tell, the story element is trying to start from the next generation era right? Like the Federation has been established and all the other empires start with a small section of planets under their control to begin with?
Wouldn't it be more prudent to allow people to start each empire from scratch. It would be alot more work, but for example Earth starts independent and it's just that planet. Your survey ship can be the nx01, you can research each ship level up past that working your way through the whole of star trek history.
You could also set up multiple independent races, like the vulcans, and just use a picture to represent them, and they could have maybe one or two ships. You could also maybe set the Borg as like the drengin and everyone teams up to destroy them. Imagine playing the Federation early in the game you encounter the vulcans, they have research abilities cranked way up, as the game continues you ally with them. They're your allies but still an independent state.
Maybe warp speed could be set up where you first research warp allowing you to travel and gradually each warp level allows you to traverse farther and faster. engines would be warp 1 to warp 10 and dilithium crystal chambers could be life support. warp five could be the standard speed allowing you to get around the galaxy and when you finally reach warp nine ships get around everywhere incredibly fast. to speed the game up in the end, you could research warp ten allowing you to go everywhere instantly!