Explanation is what's missing for me. At first glance, the Capital Wasteland is beautiful, and some of the set pieces are excellent. 'Dungeons' are fun to explore, too.
However, when one begins to question the plausibility of the gameworld, the overall experience is damaged. For instance, how the hell does Megaton even survive, let alone thrive? Sure, through trade routes they receive supplies, but you can assume said supplies consist of pre-war, irradiated [censored] for food and drink because that's all you ever see. They're self-sufficient, but aside from two brahmins, there's no agriculture, and only a ramshackle makeshift purifier to quench the thirst of the town's residents.
And don't get me started on why they'd even build there town around an ATOMIC BOMB to begin with. Yes, yes, there's some stupid-ass explanation, but it's weak, and you know the devs made Megaton so in order for the players to BLOWZ [censored] UPZ!!1I! The justification is awful.
And it doesn't stop there, either. I could go on all day about the inconsistencies riddling the game, though there's little point, as I still enjoy playing it and I've learnt to accept it for what it is -- a jumble of 'cool stuff' without any true plausibility.
I won't excuse the poor writing (really, how did the super mutants all of a sudden materialise in Jefferson Memorial after James had been and gone unscathed? And why did he leaves his damn holotapes there, anyway) and pathetic justification of just about every settlement in the wasteland, but I will respect Bethesda's effort to provide us with a huge game space, even if the majority of it makes little sense.