I own both and ME2. Story line wise I just thought that the ME series is epic. I think that the enormity and scale of story, the setting and the whole cinematic feel to it made them fantastic games. (I suppose the cinema feel is why I like Uncharted 2 so much).
Fallout 3 on the other hand is also quite brilliant in a different way. As soon as I entered the the wasteland I felt so depressed, but in a good way. That is the mood the game is trying portray. It is very impressive but it just didn't compel me to finish the story like Mass Effect 1+2 did. I think that is mainly down to the scale of the place, there are so many missions, so many towns, so much grey. It is really grey.
Graphics wise they are pretty much blow for blow. Mass Effect runs the unreal engine which is brilliant whilst Fallout 3 runs the bethesda engine from Oblivion which is highly moddable. Someone back a page said FO3 is better looking, well that is perhaps true after a couple of days of downloading countless GB's of mods for it. Once you do that you really have a Crysis beater on your hands.
As shooters they are both pretty poor I think. The team behind the new Fallout acknowledged this and have meant to have changed it in the forth coming release "New Vegas". With Mass Effect as soon as I got the Marksman upgrade it was click icon, hold left mouse button, mow down enemies: with a pistol.