It would be cool to see interesting modules like the ones MOO2 had, which seem to be something generally missing these days. The oddball weapons and other goodies.
I'm not sure I'd want to see a "unit promotion" type of system. That works really well when you're buying stock ships, but if you're designing ships (with hull space limitations) then all the goodies should be there due to you designing them in, not from a promotion type of thing. It wouldn't make sense.
The unit xp/leveling in GC *is* somewhat bland and having some kind of simplistic perk (like getting to choose between basic ship stats (att, def, etc)) might be interesting but not adding entirely new super abilities to units. Plus, you often end up having a lot of units that level a lot (in GC2 at least) and manually doing such small-scale promotions might get to be tedious (unless unit xp was scaled down to be more like civ).
I would also really like to see leaders (ala MOO2, ES, numerous others) in GalCiv III, it adds another element of customization and oomph to planets and/or ships. It also adds some potential extra stuff to put in tech/ideology trees. More, more, more!