I should point out cause you seem to be one of those "Know it all" kids, that Genocide of jews because of their religion isnt the same thing as Genoicde over cannibalistic mutants that want to rip you to shreds. The Enclave arent killing them because they are of different race/ or Religion.. they kill them because they are a VERY big threat to everyone not to mention but just because there are a few that are somewhat civilized doesnt make up for the other 97% of the bunch that will [censored] kill you. So in order to secure the future you have to get rid of all threat towards the only pure humans also only Civilized people left.. That sounds pretty damn different to me.
You're crazy, you know that?
Hitler didn't just have it in for the Jews, though those were the most unfortunate, and the most targeted. He believed in the Zionist conspiracies that the Jewish people were ruling the world in the shadows, and where they didn't outright rule, they degraded the purity of the people, both genetically and morally. Which is actually pretty damn funny, considering the little fellow was half-Jewish himself. Moving on, he also had a massive hate-on for the Romani and pretty much anyone he viewed as under... No, no, you know what, I'm not going to keep on explaining it from a Hitler = Enclave perspective, because it's different in its own way. Let's focus solely on the Enclave, and see if you get it.
Okay, the Enclave wanted 'civilisation'. They wanted 'purity'. From 'mutants'. But as you could helpfully point out to them in Fallout 2, 'pure' humanity is a relative term, especially when most of the world is a glowing pit of mutation. Okay, say you kill off all the ghouls and supermutants. Guess what? People still fight, people still hate, people still destroy.
So let's find the next level of 'impure', and wipe them out next. People with minor mutations are suddenly being killed off as threats to the new world. And who decides this level of racial purity? Who decides this level of genetic purity? Why, the Enclave of course. Anyone who argues with that is obviously a sympathiser. So let's kill them, too! Ignoring Eden's extreme-level plan, people would easily reach the same state if they were trying to run a world like how Eden wants it to be run. And /he's/ a clear-minded machine. As they say, absolute power corrupts absolutely.
The Enclave are not the 'good guys', unless you are one of them. And if you are, you're a heavily-indoctrinated xenophobe. You're no better than a crazy White Supremist, because you believe that wiping out 'impuries' will fix the world, rather than trying to get people to accept each other, differences aside. Whatever good intentions the Enclave have, it's lost as they merrily march their way to Hell by not realising how crazy they are.