Atrocities, the idea of a mod for the mod is a great idea. In fact, with you permission, I may give it a go.
Some idea I have:
1. The Borg to get bigger ship sizes.
2. A propulsion system that is not “Engines Per Move” based, but mount based.
3. Only having two sets of ship sizes: Borg and non-Borg.
4. Deleting the Master Computer component.
