I think Fallout 3 is a great game, I think New Vegas is a better game than Fallout 3 and so is Fallout 1 for that matter, but I see FO3 and FO2 as about tied. FO3 had it's huge problems though, you get railroaded pretty hard in the game and they steal a lot of ideas from previous games and rehash them in a general non creative way (see returning to vault 101 to be exiled for a great example) but what they did with the gameplay, art style and general feel of the game redeems it in a lot of ways for me.
Weirdly enough, I like a few of the retcons they made, making it so that ghouls can run now was a good change and making cars explode into a mushroom cloud I thought was a cool way of showing how horrifying the prewar world was. Not being able to drive to work everyday without living in fear of being burned alive in atomic fire I think adds to the horror of the prewar life and I liked that they pushed the 50s theme more, having a lot more oldies songs was nice too. However, some of the retcons really sucked of course, I don't like what they did with the GECK, turning it into a terraforming magic device was really stupid and of course everyone here has pointed out the amount of plot holes in the game, and there are many.
It's funny, you guys honestly challenged my opinion on Fallout 3 and it's part of the reason why I ended up liking it so much. The first time I played it I didn't notice any of the plot holes that people here mentioned so it encouraged me to go back and reevaluate by replaying it and there were moments where I was saying to myself "ah everyone on NMA was right, the writing sucks." but after a while I realized, "huh, I've actually replayed this game like 5 times now and I have to admit that I like it despite it's problems," it's main theme, environment and characters (ignoring moira brown) are all things I really like.
Earlier I said it was tied with Fallout 2, the main reason why is because I think Fallout 2 starts out really weak and gets better slowly until it turns into an incredible game. The game begins with you going through a temple that pretty much shouldn't exist, the tribals didn't build it, it isn't prewar, it's just there because the chosen one must "face his destiny" and the dungeon just isn't great on top of that. I ignore problems like that pretty easily, what's much worse for me are the random encounters in Fallout 2. They are brutally difficult for the first 12 levels, you have to save constantly when traveling because there is a very real possibility that you'll be jumped by 9 level 10 raiders that will kill you in 2 or 3 turns. Some people may like that and I get that whole, "it's a wasteland and it should be a brutal place" thing, but it's completely counter to fallout 1's design philosophy where random encounters were actually quite forgiving and the real challenge came from specific locations, like the deathclaw den in the Boneyard.
Fallout 3 on the other hand starts out really well and slowly gets worse until it levels out somewhere and honestly, without broken steel, they wouldn't be tied at all considering Fallout 2 has possibly my favorite ending in any RPG ever and Fallout 3's ending was almost insulting. I send sentinel lyons into the radiation death chamber that my dad made and I still can't continue playing the game? Fuck that, and even broken steel is lazy, your character just passes out for no reason and wakes up 2 weeks later, wut? But I still like the missions that take place after that. I liked seeing liberty prime get wasted by an orbital strike and putting an end to the Enclave for good, which leaves the game on more of a good note for me.
I really love some of the moments I've had in Fallout 3, like a conversation I had with the guy in Megaton who thought the Enclave was going to save everyone, just proving him wrong in conversation and pissing him off, that to me was a very good "Fallout moment." The powerful scene where you enter Paradise Falls and you see the kids with explosive slave collars on and you get to see, in first person, just how horrible it is to watch people get treated like less than dirt. I do love how Fallout 3 is a cheery Fallout game at times but at other times it gets really dark, really fast.
Each one has it's redeeming qualities and it's problems, but I understand why people dislike this one and I'm not going to try to change anyone's minds on it, it's already made up, and it's a very old argument at this point. Bethesda should have put more time and care into the setting, keeping FO3 in tune with the other 2 games while avoiding contradictions at all costs should've been a high priority and it wasn't, there really is no excuse for this. On the bright side, Fallout 3 is effectively a side game on the east coast that has pretty much no effect on the west coast, so if one were to prefer Fallout 3 to be non canon, it would be really easy to ignore it's existence if they wish, which I think is a good thing. I apologize for the massive post btw, never got to fully discuss my opinions on this game even though I've been stalking these Fallout 3 discussions on the forums for a while.