I have two sugesstions;
1. Various behaviors for NPRs and ability SM them
That is, I think it would be interesting to have NPR with behaviours that you can set. Fx, ability to create NPRs that will not colonize. Or will only colonize their system. Or build heavily defensively, like only PDC. Will only defend planets.
2. More political options and ability to have a wider range of relations
That is, having various forms of vassal, alliances and confederation mechanics with NPRs
All together it would give players the ability to set up wildly different games. Fx, I could make a game where all the nations of earth banded together to form a loose federation whose goal is to provide a common defence against hostile aliens, which is the player. The nations still exist as TN NPRs, but maybe they will only build civilian crafts. Maybe they will also colonize, or its up to the player to colonize for them. Maybe they will build PDC but leave all space based stuff to players. OR maybe they will also have their own fleets for defensive purposes.
I think it would be great fun if you could set up particular forms of relations between players and NPRs and also have behaviors that matches (or you not if you so choose for them to have it)