[Q]

"Finally, add Advanced traits that affect Intelligence:
Collective Conciousness - near immunity to most intelligence operations, side affect: magnify happiness shifts by a factor and magnify the limit by how much they can change in one turn. Or instead, treat every system where they have a colony as one big system for figuring out the modifiers.
Absolute Loyalty - near immunity to most intelligence operations (especially sabatoge and puppet political parties)."

That would be great IMO. But I would already be happy if the existing ability "Change Bad Intelligence Chance - System" really worked!
For the rest of your proposal I think it's too complicated and would not add very much to the game. But that's just my opinion.
However, I would like an AI intel project file were you could specify the intel projects for each race individually (like you do it for the research projects).