Different Hues/visual changes to differenciate repeat factions in the same game (Now with Pictures!)

Say you have a game with two of the same factions, even if one or both are technically custom and only using the visuals. They will be identical in colors for their ships, identical leaders in the diplomacy page, and identical names for fleets (potentially.) Being so extremely similar makes it not as interesting to play bigger games (to me, functionally it's fine, just not as immersive to play,) so I imagine it wouldn't be too tricky to at least adjust the hues on a leader's clothing, A-la Mortal Kombat alternative costumes, back when they'd only appear if you picked the same character as your opponent. 

Ship coloration could be a whole feature of its own really, but at the very least, the glowing bits and/or laser colors could be adjusted with little difficulty. Purely aesthetic variations could go a long way! Space battles would look better at least, with the two fleets having the same visual style, yet being colored or even decal-ed differently.

Taking it further, there could be narrative reasons for some changes, with or without changing the factions advantages or features. Or even have choices made in quests change things visually about the faction, similar to Civilization: Beyond Earth. But that's getting a bit far from the original idea, just ways to seperate identical Factions in the same game.