I'm just saying there should be some justification, the way that the Colonel isn't entirely evil. I think you could even strengthen the similarities between the Enclave and the Nazis (am I the only one who thought this?) by having propaganda (similar to the "THANK YOU OVERSEER" crap in Vault 101) teaching you that all ghouls are evil and stuff like that.
Yes I also think that the Enclave policies are similar to the Nazis, maybe its just a way of representing a corrupt government :shrug:
And the Enclave eyebots spread Enclave Propaganda around the Wasteland by playing the Enclave radio station all the time, the Colonel isn't evil he is just trying to accomplish what he believes in, which may seem evil to people with different perspectives
Also what is this mod going to do about companions?? From the Enclaves perspective only a few companions are actually pure:
Star Paladin cross: Evil, commits treason by working against the government, Not a pure strain of human
Fawkes: Not a pure strain of human
Charon: A ghoul, Not a pure strain of human
Jericho: Not a pure strain of human
Dogmeat: Evil, sides with the LW
Clover: Not a pure strain of Human
Butch: Pure strain of Human
Sergant R-L3: Loyal Robot
So only 2 out of 8 would be likable by the Enclave, although I wouldn't be surprised if someone shot Butch in the face because of his arrogance
Fawkes could be Brainwashed into a Frank Horrigan type soldier, here's a replacement for Dogmeat:
Scrap: a Eyebot to replace Dogmeat, he will be stronger than regular eyebots, he can get other eyebots to follow you and can be repaired with bits of metal you find (Toasters, Harmonicas etc)