The 'big cleanup' is in the works for GalCiv III 4.0.
Development on 4.0 is a work in progress as developer time becomes available (btw, we are hiring new C++ devs here..). So as we've discussed in the past, we'd really like to find a way to make modding more robust, though that's easier said than done because of the way we did our data structuring early on (there are tons of directories that the game pulls from, which all depend on which expansions you have installed).
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.
We don't have an exact ETA on when v4.0 will arrive, other than it'll probably be this Spring.