Why not? The point isn't that 'evil' wasn't ever done in RPGs. What I hate is that 90% of the time evil is kicking the dog in RPGs or just killing someone. What I am missing is evil with a purpose. Most people aren't psychos. So why do games usually only portray those?
It would be a very interesting change in my opinion. But it would require very good writing to make the choices believable. And I think Obsidian is capable of doing it.
Knights of the Republic 2, had some of the most interesting villains in a Star Wars setting in my opinion. Playing something similar to that, would be awesome.
Well, all you have to do, is to make it like in real life. The easier choice.
It would imagine that in a setting like Fallout, it is much easier to take away something, then to create it on you own. So in other words, being good should be an option of course, but it should be fucking difficult! So that the player should put some effort in to it. And sometimes the 100% good decision, should put him at a severe disadvantage.