I'm pretty sure I've already written up on why NV is better than 3 just like how I said that Oblivion wasn't a good Elder Scrolls game.
Basically, when it comes down to the heart of things, it's plot continuity. Fallout 3 just about broke all continuity with suddenly a new model of power armor out of nowhere, Mutants going straight 180 back to being comedic evil, society living without any apparent source of food or water (!!!), suddenly tons of fuel for vertibirds again, a town fucking BUILDING THEIR ENTIRE HOMES AROUND A STILL LIVE NUKE, and many other things. A lot of people praise Fallout 3 for it's more industrial feel, however, it doesn't fucking make any sense to make a town next to a live bomb without any source of food besides the one brahmin they have and scavenging/trading.