Good that you mentioned Autumn, since he is the one who refers to the people of the wasteland as US citizens, and even Arch Dornan in Fallout 2 simply refers to unarmored Chosen One a "civilian", unlike Enclave's political and scientific leadership who mostly prefer names "mutant" or "near-human". but enough of that.
And yes I definitely support whatever Colonel Autumn has in mind. Richardson, Dr. Curling, J.H. Eden and other top Enclave personnel have always been closed in their ivory towers where planning genocide is far easier as you don't know what's actually going on. But Autumn leads his mission personally and during the course of the game he leaves Raven Rock 3 times, even to such a small mission as to capture the Lone Wanderer in V87.
And what makes him a misunderstood villain for me is how to convincing Autumn to surrender. The only thing you need to do is to prove that Eden's presidency isn't legitimate, or that Eden backstabbed Autumn by relying on the protagonist for support. Which brings another good side of Autumn: he opposed the use of FEV to its bitter end, and Autumn was ready to sacrifice the Enclave's integrity to prevent a mass murder. While at first it seems he is just paving way for Eden to poison everyone, it turns out Autumn wants to control the purifier himself to do the very same thing the Brotherhood is going to: distribute water to the local population and doing so strengthen the Enclave's authority over the region.
Colonel Autumn represents an honest change in the Enclave's ideals, a new wave of thought after a total destruction because of its insane plan to kill everyone but themselves (and from what I understand, not even Enclave personnel are fully immune to Curling's FEV strain). If Bethesda had spent a bit more on letting the player side with the Enclave rather than creating more Brotherhood junk, we would have had an incredible set of character development in the form of a supervillain becoming a possibly overprotective mother bear.
The Curling-FEV Strain does not make the distinction between humans and mutants, it just kills and requires a vacination to prevent that, whilst I do like the potential that there was in Autumn as a sypathetic villian-come-hero, it's personal taste really, I would sooner the Enclave just kill everyone and have done with it. The only way for Fallout 3 to even begin to make sense is if Eden's Presidency
is legitimate, there was a huge discussion on the subject infact in on the the Enclave related threads, and the whole thing about having the PC deliver the poison is just lazy writing, the player needs moar
MORAL CHOICES!!! The Enclave has extermination camps all across the wasteland, Autumn certainly wasn't bothered about them, as were not the soldiers herding them in vans and silos to save flamer fuel, Autumn kills people to make examples and he actually killed the Enclave in Fallout 3 because he didn't have the balls to kill everyone (okay and the developers wanted a huge Raven Rock shoot-out too regardless but...), the Enclave would have won and they would have been saved. He was willing to sacrifice a good deal of the populace letting someone who went all the way through Vault 87 loose in Raven Rock. So he leads from the field, big deal, plenty have before; how dare un-combat trained, politican Richardson not leave the Oil Rig to command from the smaller, less effective Navarro?
Why is it's plan "insane", why do people just say things like "the Enclave are facsists" and "they're insane." Why? What's wrong with the idea that they wipe the slate clean and begin again, from then on, every human being would be born in a safe, clean environment without fear of war or radiation sickness and such. What does the Enclave gain from controlling the region that they wouldn't have done already, if anything, Enclave citizens will die, there resouces will be strained just so Autumn can have a clearer concionce?
In reference to the Military respecting the citizenship and pure-human status of wastelanders:
Enclave PatrolmenYou're an
illegal alien on Enclave territory. Proposition 312 orders us to shoot on sight.
Sorry, boy!
He's a
mutant spy! Take him out, team!
Die,
wasteland scum!
As a loyal soldier of the Enclave, I got orders to kill you. Hope you don't mind.
You! It's
your kind that destroyed this once mighty nation. You're gonna pay!
Don't worry, it's only some
wasteland bimbo. She won't put up much of a fight.