First basic question: how does one actually get access to the Omega Cannon/Missile Bloom/etc. modules? I've researched the relevant techs out to III and IV, but I have yet to ever see them when I try to upgrade.
Idea: this is probably too drastic of a change (and may have been suggested before), but why not be able to design starbases just like ships? This would solve the problem of obsolescent military bases in the endgame phase, and it would also be cool to have more variation in starbase design. A related idea would be to delete the starbase tech branches and derive the starbase techs from the regular weapon and protection branches. (Basically this would make military starbase techs work just like the other starbase techs--after all, it's not like there's a separate branch for "Starbase Productivity" or anything like that.)