I wish there were more areas of the ship to upgrade. I also feel like the consoles shouldn't affect ships functions but should be there to facilitate the bridge officers abilities.
So things like Warp Core, Fusion Generators, EPS Network, Computer Core, Sensor Array, Inertial Dampeners, Thrusters etc.
Along with the ones we have now, Impulse Engine, Deflectors, Shields etc.
And to stop you from just slapping all the best items on have certain types/sizes/marques limited to certain class ships or special commondations etc. Limits by credits in game, prestige, size and compatibility. So you couldn't slap a Mk X galaxy class warp core into a Nova class ship. They could have done so much more with the ships, seeing as they are 80% of the game.
Consoles should not affect ship systems as they do now, for instance having an engineering console increase a cruisers rate of turn. To increase rate of turn you should upgrade the inertial dampener system along with say your thrusters/engines. Also consoles need further expanding, giving non specific consoles maybe 1 or 2 slots that are multi purpose but with reduced bonuses that way you can reconfigure to suit the missions.
Granted they probably don't want to make it too geeky for non Star Trek fans, but come on
the vast majority are going to be the fans of the show.