Answering a fan's question, Chris Avellone discusses what he likes and dislikes about Fallout 3 in his blog. He mostly talks up tidbits and seems to avoid large-scale complaints and positives, for obvious reasons.
It's a testament to the game that for every thing that initially bothered me, there was a solution or a tool to counterbalance it. For example, I was exploring Hubris Comics, dropped my Power Fist so I could haul some extra loot, then came back and couldn't find it on the floor. Pissed. And then I remembered Dogmeat has the dialogue option to go "fetch" existing weapons in the environment and bring them back - so I asked him to go hunt down the Power Fist for me, and he found it in 5 seconds. Awesome. The game had enough options and tools at my disposal to insure I was having fun no matter what the challenges, so I can't ask for much more.
So here's the list:
The negatives: Dogmeat's breathing if you don't adjust the sound sliders. The tiny model house in Minefield not containing anything special. Anyone armed with a flamer can kick my melee-specialized ass, and thus, can kiss my ass. It was confusing to find one's way around Megaton, although it had beautiful set pieces and I got used to it. I played with a 4 ST character and regretted it, but it made me appreciate the ST boost from alcohol more (1st time I've ever considered alcohol a viable drug in any game system, ever) and also made me appreciate Buffouts. I suck at the Science minigame, which is a horrible confession for an English major. Thought Hubris Comics should have had more Grognak issues, although I really liked the fan mail and the text adventure game in there. Didn't like not being able to kill Amata or Andy the Robot at the outset because I hated them both. I didn't like that the first potential companion was a bad karma companion and expensive, but then the twin goals of being an **** and scrounging up a thousand caps became bait and a challenge in trying to get him - when I got Jericho, I felt like I'd earned him as a companion. I think Repair became too valuable as a skill, but it's better than the special case it was in Fallout 1 and 2, so I'd rather that than it remain a broken skill (like Doctor in F2). Maybe because I'm approaching it from the development end, I didn't care, but I think the level cap turned a number of people off, as did not being able to play after and continue the game until Broken Steel came out. Some of the locations I think broke the 4th wall (Dunwich, which I actually enjoyed playing, just not the premise).