Okay, so I know what the current hardcode limits are.
These are the ones that REALLY need to be expanded-
Mesh count- currently it is 400. Double it, or even increase by 250% (2.5x, or 1000).
Texture count- this one is the biggest one IMO. Currently it is 1000. Triple or quadruple it.
WeaponType count- currently 3. This one I would LOVE to see bumped up to 5.
Squad count- I think it is excellent that it is currently at 4. But that isn't quite maximizing the space in the squad management menu. I don't think it would be to hard to kick it up to 5.
EDIT: and add two new banks- UP (dorsal, the top), and DOWN (ventral, the bottom).