The Enclave were far from good guys. They attempted genocide multiple times. And those power-armored dudes opening up vaults just to slaughter its inhabitants? Yeah, that was the Enclave. In Fallout 2, they were straight-up evil.
In Fallout 3, they were a little less evil and I will admit that Colonel Autumn would have been a good leader. Had we been able to side with him, I may have done it. He was against killing off all mutated people like Eden wanted, he was far more reasonable than the rest of he Enclave leadership, and ultimately he wanted to help the wasteland and restore America. All of those are good things. Yes, he was still ruthless, but that doesn't bother me too much given how harsh the wasteland is.
In a way, the Brotherhood did kind of fuck things up for everyone when they took down Autumn's Enclave. Autumn was basically trying to do the same thing the Brotherhood was doing. He just wanted the Enclave to be the ones responsible for saving the wasteland because he believed it would rally the people behind it and help restore America, and honestly it would have probably worked. The Enclave also had more resources to restore the wasteland.
My problem with the Enclave is this: They were evil as fuck in Fallout 2. And a lot of those guys and their descendants are still around, and just as fucked up as ever. Autumn is actually something of a rarity, it seems. So while I think Autumn would have been a good leader, who could have made the Enclave into something better, I have to wonder what will happen when he's gone. Would the Enclave just go back to its old habits? So then you'd have everyone under the control of genocidal lunatics who may try to finish what the Enclave could not finish all those years ago. I don't know if I want to risk that. At least with the Eastern Brotherhood, we know that most of them are good people. And a lot of them are regular wastelanders who know how harsh it is in the wastes and have the motivation to help make it better. The Enclave are a bunch of dudes raised in bunkers by racists dudes hellbent on world-domination and the extermination of all things mutant. No thanks.