I liked fallout 3 better overall, but both games do have issues. Fallout 3 froze on me quite a bit, especially in point lookout, and NV's framerate can slow down to .5fps when you save file gets big.
Some people have had better luck not seeing issues starting a whole new game in the GOTY and Ultimate editions rather than importing old saves from the vanilla versions. Still, despite the issues, both games are well worth playing.
Glad DmC shipped a million copies and was a success. Supporting risk-takers and change is how the industry grows. http://imgon.net/di-CFMD.gif