Mods that improve the AI, or that add more units. Even better, a mod that splits affinities into two subaffinities, for instance:
Harmony:
1. Mutated units, uses genetically enhanced/mutated soldiers that are fairly unpredictable. Their soldiers gain offensive bonuses the more units there are next to them that isn't the same type as the soldier gaining the bonuses.
(Unpredictable meaning due to unstable mutations, they gain minor bonuses in certain situations like in forests, while beside a canyon, fighting against a city etc.)
2. Alien swarms, selective breeding done to pre-existing alien creatures to make them stronger. Zerglike, and have the ability to spread a miasma-dependant creep-like substance that improves tile yields while preventing improvements from being built on opponent's terrain.
Supremacy:
1. Massive war machines like the current ones and several unique humanoid mecha generals of which only one can exist in any given civilization at a time, but they grant various combat bonuses to units surrounding them in a radius much like boosted great generals.
2. Completely AI civilizations that rely on swarms of nanobots and the ability to combine certain weak soldiers into increasingly powerful 'armies' that gain extra health and a little raw strength, example:
Two Tier 1 swarms combine to make a Tier 2 swarm, which then combines with another Tier 1 swarm to make a Tier 3, which combines with another Tier 3 to make Tier 6 which is the highest possible. They start out at 2 being the maximum, but with certain techs can increase that to 6.
Purity:
1. Human-based armies with a mix of heavy artillery that can't completely kill enemies and soldiers that mop up heavily weakened-by-artillery soldiers with ease.
2. Purely offensive armies with more raw strength, but not a lot of specialization.