I think the three Affinities could be made to work just fine, the problem is that currently the mechanics force confrontation with shared affinities, while permit peace with different ones.
At the minimum, having more points in an Affinity than another Civ should generate progressively greater amounts of hate with that Civ. Beyond that, I'd like to take some of the ideas from Dynamic Affinities to make the different Affinities terraform differently. So Purity should make food and production improvements, Supremacy should make energy and science improvements, and Harmony should raze them all and spread miasma; and all those tile improvements should generate their respective affinity points, and drain opposing affinity points. This would encourage more vicious wars with more raze/plundering when fighting opposing affinities.
I agree on the first. the way the game is set up, you most certainly will go to war with your own affinity than with another, two out of three times, due to thirst for resources and given that, by and large, it is that resource availability that determines your primary affinity, it shows us that this game is a conceptual mess.
First because each affinity has a high ideological content, at least if you go to the pedia.
Second, because all affinities seem to go nuttier the further you get to level 18 affinity, again by lore this. look at the entry on the LEV Destroyer...
Third, each affinity is doing their own thing towards victory. there are no sparks of conflict other than sheer greed of resources, of land, of building an angular throne...
Sure you get a few 'your affinity is not mine and I am worried about it' but it doesn't end up in DoWs either. at least in the lower difficulties, including "normal"
I think affinity resources are a stupid idea, or rarther that you only need your Affinity Resources to build advanced units. they should be an eclectic mix, if favoring your local resource, of different advanced resources (another name for the aff. Resource).
that way you have what the other has and has one more nail towards DoWing...
End games should be more involved than what we currently have. the way it works each faction is closed into itself building their endgame, it makes for a very boring late game. perhaps a good idea would be for the location of the endgame wonder being at preset locations/features of the map (but not only one location in the whole map) for instance the gates need to be in between the tropics and require a certain elevation or the mind flower needing a particular brand of biome or the signal whatever needing an equatorial mountain/hill.
This is a 4x not simcity!
Ah, I went full rant mode, I'll stop here.