No...  No offense, but it would ruin the current concept of everything..  The only thing I could imagine this working for would be orbital turrets...  If you redid them, you could have those as customizable...  Perhaps some be anti-cap and have others as anti-medium...  Idk, just an idea...

for Cap ships, it MIGHT work. MIGHT mind you. It would take a bit of fiddling (doesn't it always?), but it could possibly work.

True, but maybe there could be a new kind of turret that could be upgraded with three different kinds of weapons (anti-SC, anti-Caps, anti-frigates/cruisers) and a shield/HP upgrade. They should also have three upgrade slots (four with research)

well you could make it a research to unlock a certain ability?

I have to say some of the responses in this thread offend my modding sensibilities.

Mod what ever you want to Mod, that someone else doesn't want the system changed is not a valid reason not to do it. The whole point of Modding is to change things.

mini rant aside

Your main issue whilst attempting something like this is that the modular nature of the starbase is specific to starbases. So it depend on how you want the system to work, if you want ships to have only one upgrade of a possible two or three, then you're essentially screwed, If you simply want to be able to upgrade the ships chunk by chunk as it were (say offense, defense, engines), then a mixture of research and unlocked abilities is your best bet, or alteast most player friendly bet, firstly because it means you can limit the research to a specific type of ship, secondly becasue it means you could upgrade the ship meshes as it happens (which is always cool), and thirdly because upgrading individual ships (even if feasible) would be tedious.

thanks for all the imput. and the titan idea is a good one if you don't minde i'll work on making that.