1. NCR is not exactly saints either.
2. Depending on personal perspective one could consider some of their laws "evil".
3. NCR makes it's own people suffer due to taxes and valuing the rich above the common folk.
4. Again, depends on perspective, but I'm guessing Khans wouldn't exactly call NCR good.
5. Lots of the people in the NCR are angry about their government or officials or laws.
If Legion is to be considered evil then so is NCR.
Maybe Legion is a tiny bit "more" evil, but evil is still evil.
I didn't quote this, but you said "The Legion isn't chaotic evil". IMO you're right. But they are very much Lawful Evil.
As for the NCR, if one wishes to continue with D&D allignments, IMO NCR is Lawful Neutral, with some leaders leaning toward good, some being corrupt and leaning toward evil. The problem with the NCR is they are being imperalistic long before they have the strength to expand out from California. They basically bit off more they can chew by securing the Hoover Dam to help power their nation, and then finding that they are stretched too thin, the way I see it anyway. Look at the frequent complaints of every outpost commander at every camp. They need more troops, and they need more that aren't just recruits.
Having said that, IMO the sins of the Legion are still much greater then the sins of the NCR, although yes they did mistreat the Great Khans. The Great Khans aren't exactly saints, but they aren't horrid. (To continue to use D&D allignments, I'd put them True Neutral).
My personal take on each faction. This will be short:
Yes-Man: Well, YOU become the dictator. You could mean well, you could be a tyrant so it's pure RP. Plus there's the factor of Yes-Man becoming Skynet and/or Hal 9000. He may come back after becoming "more assertive" just simply that, have a bit more backbone. But he may come back and send a dozen Mk 2 Securetrons on your tail too.
House: Well meaning, but a complete despot and although he does have a grand plan, he isn't seeing the individual in his grand plan. I don't think if let's say Goodsprings or Primm were to say "Screw you House, we're independent" that he'd send a half dozen Securtrons out to waylay the town. In fact if memory serves he sends Victor back to Goodsprings to watch over it. But at the same time, people are pawns to him too, if someone stood in the way of his major plans to control and run New Vegas, he'd have no issue getting rid of them. He's obsessed with his plans, period. And his plans for the most part, with only some exceptions don't take into consideration anything much outside of New Vegas either. (If memory serves he sends Victor back to Goodsprings due to them helping the Courior, not due to any desire to protect the town past that).
NCR: As stated above, they are perhaps well meaning but they expanded WAY too soon and are spread way too thin.
Legion: A tyrant that thinks he has the right to rule, period. And thinks his way is the only right way. Caesar doesn't want to listen to opposing viewpoints, he just wants people to agree. And will try to rule period, regardless of what it takes. I can't see how anyone can call any faction willing to set up a lottery, winner lives, second place lives but with their kneecaps busted in, rest enslaved or killed, one burned alive on a pyre made of tires only "less moral". That's just evil. Even if many in the town I'm thinking of were Powder Gangers, whom are very far from being saints obviously.