The trait-gain I'm going to be looking at, rather closely. Already have to rewrite portions of it to get it to work properly with 3.19, so I can tweak it while I'm there... And write down EXACTLY how it works, to put into a Concept section.
I like Xienwolf's suggestion... I think most Major leaders should be fine as they are. Minor leaders should be given traits that are wildly different... How about an arcane-focused Elohim, for example?
The Emergents are essentially meant to be challenge-mode. They're strong in one area, but most others are weak... What I'm planning on doing, is having Minor/Emergent leaders set, by default, to not show for the AI or Random leaders. Then, two game options that allow them. Won't affect anything if you select them manually, but being able to control their appearance should help the AI.