To me, in NV they tried to do two things at once, and failed. FO3 was definitely all about the waste part of the wasteland, and I LOVED it. Before NV I did think it was a little silly that nobody planted any corn, but it wasn't enough to distract from feeling hopeless. You're a kid thrown out into a completely messed up world, the first town is made from garbage, the raider armor is made from scraps, wildlife is mangy and feral, not even the water is safe, super mutants and feral ghouls want to kill you, etc. Even the BOS with way more than anyone else is struggling, the Citadel is half scrap as well. It's always dragging you down, no hope, ever.
Now NV tries to inject some civilization into that, but tries to keep the wasteland as well. And in my opinion fails. A perfect example of this is Primm. As it is it would fit right into FO3, two beat up buildings with people who are struggling and others who want to kill you. But that's mitigated my the NCR being nearby and it was supposedly a real town. Other than the bunch of houses that are so easy to miss there is no evidence of a town. Outer Vegas is even better. The supposed oasis where hundreds or thousands people flock has guns-r-us and implants-r-us just plopped outside the gates. Inside is even worse, there just aren't enough people, there's no place for them to live (remember how everybody had their own house in Megaton? Sure they were filled with useless stuff but it made Megaton feel real), and plopped in the middle of that is lazors-r-us.
And the super mutants, sure the ones in FO3 didn't have anything to do with the master, so what? That's what you're picking out that makes no sense? It's fun, and none of this makes sense. And Liberty Prime. Yes that's silly, but an army of unicycle robots isn't? I can go on and on, but I liked FO3 better. If you like NV better, that's fine, I can see why, but I liked the more desolate feel of FO3.