I've actually been replaying Fallout 3 a fair amount recently, partly to see if I really gave it a fair shake last time... as I really really disliked it.
Thoughts a second time around?
It's still not great, but not as bad as I remembered it being.
The continuity is completely broken betwee Fallout 1/2 and this and doesn't hold up on a logical level. This is a bit of a fanboy protest, but still, if you're doing th sequel to one of the beloved RPG frachises, you should at least be able to keep it roughly within the guidelines. And that's without the fact that it lacks the "feel" of either of the earlier games... and Fallout 2 was criticised for lacking the feel of the first.
The plot doesn't make sense in the slightest and is outrageously railroaded... which severely limits roleplay value.
There are some huge bugs/glitches in there. Some are gamebreaking requiring massive save/load style play to get around. Others are frustrating... I came across the levitating Deathclaw about 6 times (when a Deathclaw just suddenly flies into the air and disappears).
The vast majority of quests are pretty banal, consisting of fetch/carry quests with slightly different bad guys to kill each time. There are some gems in there, but they're not as developed as they could be. There never seems to be a real consequence to whatever choice you make. It also feels like there could be so much more. Take megaton... read moriarty's notes... and other than the drug dealer plot there's little you could do. There's a seemingly simple quest between the "good" bar and the "bad" bar (so simple it was even in Fallout 2...)... but there's nothing.
Gameplay is pretty much run and gun. Sneaking is of limited use, Speech seems to almost entirely be about getting yourself a bigger reward and your responses only ever seem to break down into 3 options: Boy Scout, neutral and arsehole. Hell, comparing the way you convince Eden to blow himself up and the way you convinced the master in Fallout 1 is almost sad as you see how the dialogue has regressed. Let alone if you throw in talking about Jet creation in Fallout 2.
The way karma has been changed (and reputation removed) doesn't make sense. Hell... you kill all the ghouls who murdered the residents of Tenpenny and you lose karma? I lose karma for kill a group of mass murderers...? And that's without the issue that why would the people in Rivet City care that I stole all the food from the Republic of Dave (without anyone seeing)... and how would they know? The old reputation (for how each area saw you) and karma (for the good/bad you actually did) was far superior.
And the ending. Oh god the ending.
I had fun replaying it. There's a certain satisfaction of the slow motion VATS headshot that sends an opponent flying, or pinning an arm to a wall (although it gets tiring pretty quickly) and wandering round the destroyed area just checking out the sights is still pretty awesome. But I can't really play for more than an hour at a time without getting bored...