New Vegas had the better Main Story and DLC's. Fallout 3 had a better world space, atmosphere, side quest. The speech check system is vastly better IMO. It's DLC's aren't as strong as New Vegas's where NV's only meh DLC was Honest Hearts. FO3's only real good DLC's were Zeta and Pitt. Broken Steel should have been apart of the game from the beginning and Point Lookout suffers a lot of the same issues HH does in it being a bunch of fetch quest and a boring story that shoehorns you into choosing a side when you've only been on the island for a day or two, that's not even taking into account how horribly unoptimized the world space is.
All in all, FO3 is my favorite, but only when it's in the NV engine. NV introduced a lot of neat features that I simply couldn't ever play without like ammo crafting/recycling, cooking, I forget if FO3 had crafting beyond schematics but more crafting. Ammo switching. AP and HP rounds are such a game changer in their respective situations where they excel.
General Discussion of Fallout 3 unrelated to Tale of Two Wastelands