I saw someone somewhere suggest giving a penalty to how quickly you progress in the empire tree based on conflicting affinities, as a measure to weaken rainbow builds. A softer approach like that seems like it would be more appropriate.
#Affinities still don't feel like they matter enough. Here is my proposed solution:
peak sapphire
delicate barn
I'd rather see increased bonuses for having a very high rating in one affinity, personally. A big part of the fun for me is mixing tomes of different affinities to create various builds, so I wouldn't want to see that restricted, but at the moment there's no real incentive to focus. You can reach the end of the empire tree in an affinity well before the end of the game, and once you do, there's nothing left.
There could be repeatable capstone empire skills for each affinity, which increase in affinity requirement each time, or maybe some way to use excess affinity generation as a resource.
round ermine
I'd rather see increased bonuses for having a very high rating in one affinity, ...
i think a massive expansion of tome selection and multi-affinity tomes with some possible extension of affinity trees could help. i think with more tomes to choose from there might be a possiblity of tying the unlocking of high tier tomes to quests or some other prerequisite to require more dedication to reach high tier tomes. also governors should be more impactful than they are.
raven flume
While i understand where you are coming from, and some others probably think similar, destroying affinity combinations like that goes against the spirit of the game, where we can customizate our faction a lot. Besides, mixing affinity/spheres Was so far possible in other aow games too. I could pick 3 life and 3 death in SM if i wanted.
peak sapphire
Another thing to keep in mind is that your Ruler's Signature Skills give affinity points, so any change to the impact of one-off affinity points has pretty massive implications there. (which I sincerely doubt the AI would be equipped to handle).