Quinch, I went through your work and applied it in the FMP. I took: all Snakemen (except for the Medic, which doesn't exist in the game) and shuffled the colours a little bit, all Floaters (made bigobs too), Sectoid Commander (not the other ranks, I didn't want all of them to wear circlets).
I didn't touch the Mutons because they were already using custom sprites, Reptoids because I want completely new sprites for them, or Chtonites because I can't see why they would different in colour.
Either way, I don't mind. You could pack both rulesets into the same zip file and let the players turn it on or off as they want, so there's no need for compromise.
Maybe, but FMP is supposed to be a no-brainer to install, so I didn't want to burden the players with such decisions. Besides, I think additional visual cues are fair in this case, with live capture being crucial and so on. Veterans already have a fairly good idea on who is where.