FONV has a better main quest, better gameplay, and (in general) better dialogue.
FO3 has better sidequests, and better exploration.
So make of that what you will in your decision. Then again, if you're buying it through the Steam sale like I assume you are, what's to lose in $10?
--
Will not remove this line of my signature until the Seahawks, Jazz or Rockies win a title (Started 5-16-09)
Yes, I know I'm never getting rid of this signature