Couple of things that are kind of lacking for me in this game as far as a realism standpoint goes.

Engines:
We're buying impulse engines, and they are labelled as such. Therefore warp engine purchases should be separate, and have stats on their own rather than being combined. There's always a tradeoff. Ex: Borg SUB-TRANSWARP engines do a better job at transwarp speeds than they do at impulse or regular warp (imo), despite their label.

And this leads us to:
Power Levels:
A ship's power is dependant on the warp core and computer core. I believe these two should be separate purchases on their own. Buy the warp engines for warp travel and it's effect on power levels. And the computer core can boost the ships effects on systems and processing, leaving the deflector dishes to be more specialised.

This can lead to more creative ship customisation, and the ability to really create the ship you need to play with (money permitting, which by the way, was supposed to be abolished in the 24th century - but this IS a game after all)

Also, this COULD lead to all the old ships being relevant again. I used to be able to fly and succeed in missions with my old USS Concordia, but now, even with higher upgrades my rank barely allows me to survive these missions at the same difficulty.