Lately I've been hugely dissatisfied with how the Awakening implemented the Academy empire and I've been tinkering with the idea of replacing it completely.
My main problem is I am unable to change Empire 13 which is the Academy faction from an AcademyFaction to a MajorFaction managed by the AI. I want to override it completely with a regular Major Faction I will mod in its place. As of now I think Empire 13 would have to stay as it is and I'd have to add a new AI Empire and give it the Academy system somehow (my guess is a quest could do that) and manage the functionality lost (fortunately it isn't much more than quests, title management and Nakalim system donation which will probably be the most tricky one). The list of problems for now is:
1. Is it possible to add an AI-managed Major Faction on top of what's already in the game?
2. Is it possible to give a specific Empire control over the Academy system with a quest?

If answer to both is Yes then I'd seriously think about revamping the system (which, quite frankly, could probably work to some extent without Awakening active).