All of the factions are basically "trying to make the world a better place" they just have different ideas of how that should happen. The Enclave in Fallout 3, I thought, was very nicely done in that they *weren't* just omnicidial maniacs. They had a plan. Their poison wasn't engineered to kill *everybody*, only those who had been genetically compromised. You could argue that it was in fact a repentant goal since they were the ones that caused the problem in the first place with the FEV. It was a plan with different priorities than most people would consider proper given that we know ghouls and mutants are intelligent reasoning beings, but consider this: the Enclave has air transport, satellite communications, high tech armor and weapons, clean water, and tons of other things. Their methods in achieving this strategy are questionable for people not officially part of the Enclave due to their reckless disregard for personal rights and property (and downright unsurvivable for mutants and ghouls), but the fact is that they have more functional technology and a higher standard of living than anybody else, and their plan is probably the most
direct route to getting humanity on a road to what it once was. It's also worth pointing out that while the Enclave did build many of the vaults with radical scientific experiments running in the background, they did build many vaults that did exactly what it said on the box: protect the inhabitants through the war and beyond until the outside world was capable of sustaining them.
The Brotherhood of Steel, likewise. They are slightly xenophobic and bigoted and really don't have any time for everybody else, but they have a plan to save humanity. Just not their immediate neighbors. Their mission is to acquire and preserve as much technology as they can, and they are extremely pragmatic by recognizing that the only way they can take away powerful technologies from people that would misuse them is to have a bigger stick and use it freely. This goes more for the West Coast chapters, of course; the Eastern chapters have that whole schism that leads to the Outcasts. I've never seen the Brotherhood as evil in the slightest bit. If their strategy betrays a total lack of faith in humanity's ability to not blow up itself and the little that is left of the old world, it's understandable because humanity keeps proving them right.
The NCR can easily be cast as the inept, accidental villians of F:NV, since they were the ones that moved in for selfish reasons and attacked the Brotherhood, which has destabilized the region to the point that the Legion is now lurking on the flank. The Brotherhood was getting along just fine before the NCR moved in.
The Legion... From what we have *seen* of them, I don't like them at all. But like others have said, the only part of the Legion we have seen is the army, and from the perspective of a contested territory the invaders are always the Devil incarnate. How much of what we hear about them is actually true, and how much is the uneducated fears of the Mojave locals or the propaganda of the NCR (who, you will remember, is fighting an unpopular war against them). I would love to see more of their culture and give them a chance to make their case more fully before making any kind of final judgment on them. Caesar himself comes across as intelligent and charismatic....perhaps a bit tweaked, but that's hardly unusual. Trying to say that the Legion's empire as a whole is good or evil would be like trying to participate in European politics in the 1600's based on what you know from watching Jamestown.
Anyway.
Just the fact that we can even have discussions like this illustrates what a great job the designers of the Fallout games have done.