Rather than adding in a giant pile of new ships with every expansion (which will eventually make the game impossibly huge to comprehend), add in some additional depth to the ship types we already have? I know global upgrades have been rejected before, but I think it should seriously be considered. For a decently steep upgrade cost (3000 or so), you can upgrade damage, speed, armor, or hitpoints by 10% or so (maybe some other metric for armor, since 30 armor usually doesn't make much difference?), or a special ability. There's only one upgrade in each category to keep it simple and keep someone from making their basic fighters UUUUUUBER. Another upgrade branch could be used for turrets, possibly one for command stations to give them access to exoshields or some such, possibly one for starships. Rather than adding it all in to the Science Lab foldout, a new building could be added as an Upgrade Station, which would be a relatively cheap stationary building. Man, what if we could upgrade harvesters to have tiny defense cannons that can destroy those annoying one or two minipods or etherjets that are flying around constantly picking off your harvesters and not letting you auto-rebuild?
Some examples of special abilities upgrades:
Basic Fighter: Increase armor piercing.
Bomber: Increase damage multipliers by 1.
Frigate: Decrease reload speed.
Chameleon: Allow "debris form" while moving, but with very long "recloak" time and doesn't function in short range to enemies (3000 range or so).
MLRS: Increase missile shots by 2.
Bulletproof fighter: Becomes immune to an additional ammo type (to be determined).
Tachyon Microfighter: Increases tachyon range.
Laser Gatling: Increase ship cap by 10%.
Autocannon Minipod: Increase armor damage.
Raptor: Radar dampening 10000 or so.
Infiltrator: Radar dampening 8000 or so to keep them from getting wasted by fortresses.
You'd have more differentiation between ships, and more ability to choose differentiation between ships; rather than upgrading your frigates to level 3, you could instead upgrade your fighters to have increased damage and increased armor piercing, but you end up with a bunch less ships in play which can hurt you in the long run if you spend too much knowledge on upgrades. Not sure how you'd program in global upgrades like that though.