The "big cleanup" is the plan for v4.0 of GalCiv III. It's in progress but it's slow going because of developer availability (btw, we are hiring new C++ devs here..).
So as I've discussed in the past, I'd really like to find a way to make modding more robust though that's easier said than done because of the dumb way we did our data structuring early on.
Basically you have lots of directories that the game pulls from which all depends on which expansions you have installed. It's a pain.
When someone buys GalCiv III today from Steam, they actually get GalCiv III + Crusade + Retribution. That's because we really want to focus on the assumption that everyone has Retribution going forward (or at least Crusade) which simplifies modding.
I don't have an exact ETA on the v4.0 version other than it'll probably be this Spring.