I'd go with Fallout New Vegas rather than Fallout 3. Fallout 3 is basically Skyrim, just in a different setting. New Vegas has actual good plot, it is Obsidian's work rather than Bethesda's after all. Gameplay's meh, still on the ''Gamebryo' engine.
Haven't played 'Alpha Protocol' - another Obsidian title - myself but a lot of people here claim the story's pretty good. From what I understand, the gameplay's a mess, though, so I don't know.
Dragon Age: Origins is another title I'd recommend (though you've most likely already played it, considering you were talkng about Mass Effect). The plot itself is pretty generic, so are the characters, but it's all presented really well. Combat's pretty tight, too, though they decreased the difficulty with patches (kinda like in TW2). Definitely skip DA2, though.
Batman: Arkham Asylum is another good one, don't know if you've played it. Story's alright, they nailed the setting and characters, combat and stealth are fun as well. It's just an overall nice package. And it's Batman.