Unlike previous games made by Bethesda similar to it in some ways that were crappy and overrated beyond sanity or any rationality (cough)Oblivion(cough) Fallout 3 really was pretty great, and worked well with the way they made the world and the game mechanics. It actually felt like everyplace was unique in it's own way and it didn't feel like a whole lot of nothing, (Unlike Oblivion where 90% of the game felt like almost the exact same dungeon and after exploring a few places you didn't care about anything else.) so exploring was actually a little fun, most of the missions seemed enjoyable to do and fit with the plot and the setting, and the plot that went along with it fit in and didn't seem like it was tacked on. Maybe most importantly it seemed to fit in with the Fallout universe's feel, like the previous Fallout games did.
There were a few things I didn't like about it though. I still like the traditional RPG game mechanics better in previous games and wished it would have went with it in this one, but what they did wasn't badly done. Caps in the game can be hard to come by, especially at first and dragging every piece of equipment to sell can become a pain in the ass if you go that route. I know it was an post-apocalyptic world but there were times that finding ammo instead of doing fun stuff was grating. Shops only can buy so many caps worth of things, and in fact I think there is a strict limit to the number of caps and things from non-spawning people in the entire game. Fixing things seems like a really good concept for the most part, but can also be a pain in the ass some of the time. Trying to keep that one power armor you find fixed made me almost not want to wear it. (It didn't helped that they nerfed power armor in this game to the point a lot of people suggest not even having it. I can't help myself though, it wouldn't be Fallout without walking around in it.)
Sometimes in a game for the sake of it being a game or to keep it fun they have to surrender some realistic aspects and virsimutitle to keep things fun and I thought in some areas they should have done that. At the very least it would have been nice to have my complaints above tied to difficulty level or even a lot better just an option to turn them off somehow.
One of the things I hated most of all was the rubber band AI and the scaling of opponents to your level. I would have much rather have them be a certain strength, plus in a lot of instances it made no sense. Even that wasn't remotely as close to being as bad as it was in Oblivion though.
About the only other thing that really bothered me was the ending, especially if you played a good character (I never play bad ones in any game that gives you a choice). Not only do you have to pick between two bad choices with no alternative even though logically you could think of several, but depending on what henchman you have following you around it can also fly totally in the face of common sense.
All in all the positives outweigh the negatives by a substantial amount.