I thought the story in FO3 was a good
story, but it didn't make for a good game story, because it railroaded you along to each next stop with no real decisions to be made. It would have been much better as a movie or novel.
For instance, consider this, you only have 1 truly meaningful choice to make in the main storyline of FO3:
Spoiler Whether to put the FEV in the Purifier and or whether not to.
That is it. The rest of the main story is the same every single time without fail.
In New Vegas there are 4 "critical paths" each of which can remain separate or intersect and weave in and out of each other, depending on your decisions. That right there is 4 replays worth of story. Not to mention that there is massive variation and replayability within missions themselves. In fact, some critical path quests in NV can branch out the story in another direction because you FAIL them. The critical path the quest was on doesn't end, you don't have to load and retry the mission. The game adapts to your failure and you get NEW story for screwing up.
New Vegas is a much better GAME story, because it is all about your choices. You truly determine everything that happens in the story. No Daddy NPC is giving you stepping orders constantly. You want to do something, you can do it. Don't like what your quest-giver is asking you to do? Don't do it, or tell them you'll do it and betray them, or trick them into thinking you've done it and continue on working for them, etc.
In FO3, the Enclave was always the enemy. Even if you sided with President Eden in the end, the Enclave remained your enemy. In New Vegas, I'm on my second playthrough (I was eager to try out different story paths and other builds after putting in 50 hours and went ahead and finished the game with my first character). The major enemies for my first few hours in my first game, are now my main friends with their own quests and storyline, on my second playthrough. All because of different choices made on my part.
That equals better storyline in my book.