I'm one of those of who thought Fallout 3 was merely ok, but rates Fallout New Vegas as their game of the year.
The game still uses that ol engine, along with the flawed(but vastly balanced and improved this around)FPSRPG combat, so at least on the surface it remains a similar experience.
However to a discerning gamer, these games are designed very differently. Fallout 3, like Bethesda's other recent games, gives emphasis on exploration with the expense of both narrative and in depth RPG elements. If you like wandering the wastelands aimlessly in search of coves of treasure and dungeons full of baddies to splatter, then Fallout 3 is your game. Its a very flawed game from both a quest, writing(honestly a lot of the dialogue is laughably bad), and world-building perspective but its good at what it excels in.
Fallout: New Vegas represents in many ways a return to form in spirit of the original games. The game is far more focused on cities/towns and is much more quest/narrative oriented. While the game still encourages explorations, most locations have a specific purpose within the overall conflict. You learn about the plights and ideologies of the various factions at work in the wasteland, and the complex power dynamics involved. Skill placement and S.P.E.C.I.A.L are far more important this time around, because they usually influence how you approach questlines. You also have skill check dialogues that don't make you cringe, and make you feel ashamed for purchasing the game. Obsidian's strength is writing, and it shows in this game.
I vastly prefer New Vegas because its what I want in RPGs. While loot is cool and all, having a sophisticated well written RPG is what I need.