The Legion regularly does atrocities to random people or just to people who were on the wrong side like the NCR. The legion on the other hand are the most evil faction in the entire game of Fallout New Vegas. The Independent ending has some negative effect for groups like the Followers of the Apocalypse but so actually in the long run it allows the region to develop its own indepedent culture and strength. The NCR apologizes and feels shame actually over the mistakes they make like Bitter Springs, as with any large entity they are prone to corruption but the positives outweigh the negatives geneally.
The NCR isn't perfect but that doesn't mean they're neutral or bad. The two bad routes are Mr House and the Legion The two good routes are the NCR and Independent. I would say they're just more fleshed out as entities in the gameworld.
