You do raise a good point, but I have a counter; a good RPG is not one where you can do whatever you want without consequence, it is one where you can do whatever you want BUT MUST FACE THE CONSEQUENCES!
Let's take your Powder Gangers example - Goodsprings hate them, NCR hates them, just about anyone who isn't a Powder Ganger hates them! Ceaser's Legion is much the same. To use a real-world anology, how do you think people would react to you if you openly signed up to a terrorist organisation? Even if you didn't do anything to them, they would hate you purely because of the company you CHOOSE to keep.
Yes, the NCR are mostly scum, but the alternatives are, in the eyes of most people, a heck of a lot worse!
The problem still remains that the Legion was included as a major, player-backable faction, and it is game-breaking to actually back them.
Why would sane person choose to cut out 80-90% of the playtime on a game meant to be explored and RP'd through in exchange to back one single faction?
Playing an "evil" character should not have been a punishment to the PLAYER, and it is. "Oh, you're evil. Well, guess what, now the game is 500% less fun for you."
I think the devs pretty much assumed that if you are choosing the Legion as your ally, you are pretty much playing an evil character. So by that standard, you have to include quests you can do for the Fiends and the Powder Gangers.
This is what I would have liked to have seen.
If you are building a reputation as a murderous thug, then the murderous thugs should recognize you as a potential ally and resource. You're a beast, remember?
The game is set up to take advantage of what is essentially a POLITICAL atmosphere. There is a lot more to gaining territory and influence within a region than just bulldozing through killing everything in sight. The game is set in an area where BOTH factions are invaders. Where are my missions to turn towns against the NCR? Where's my clever diversion into getting the Khans to do what I want? Why is it the Powder Gangers, who were smart enough to start a prison riot and (with my help) stop the NCR from regaining control, are too stupid to make sure the NCR doesn't try it a second time, or sit there like a duck in the water waiting for Legion to pick them off? Why would the casinos not seek to save their sorry asses in light of a failing NCR campaign?
Even better, I would have LOVED to have been able to actively change the landscape of the game. I.e, by helping the Legion take over NCR camps, I could have slowly LITERALLY given the Legion control over areas. And when the Legion set up camp in new areas? All those lost NCR quests that occurred there would have been replaced with Legion counterparts.