If Fallout 3 had roving motorcycle gangs, and cars could function as legitimate cover (rather than being exploding barrels), and the vault dives were deeper, it'd be no contest. As is, I can only say this conclusively: Fallout 2 is better than Mass Effect. Fallout 3 and Mass Effect are about on the same level.
Though, at least it was nice to have actual weapon choices in Fallout 3; in Mass Effect, there was absolutely no reason not to use the Assault Rifle at all times, except for maybe the first few levels if you're playing a class without the assault rifle skill. And VATS earns some points for being able to shoot grenades and rockets out of the air.
Haven't played Mass Effect 2 yet, so no comment.