New Vegas is a far better game in just about every way.
This. It's like Super Mario 2 compared to Super Mario 3, one was the odd one out and was just kind of an awkward entry, while the next set the series back on track. FNV inherits the engine but just about everything is done better.
That said, they both have a problem with scale. Maybe due to that engine. Factions and smaller towns (i.e. not New Vegas or Washington) seem too small, though FNV had the sense to offer some sprawling, complex environments. Even then, things like Fortification Hill feel too small and especially underpopulated for what it's supposed to be.