I'd definitely agree with Bioshock 2. I'm never a big fan of the "Oh but it isn't as good as..." mentality anyway. I know, I've played it, are you expecting me to just go back and do it over and over? I liked the first one more, but they're both great games and I have a lot of time for the series.
Fable 3 could have certainly been better, and wasn't helped by old Peter there and his fantastic claims, but I saw people claiming it to be the worst game ever made. These people must lead very, VERY sheltered lives. As far as the sanctuary, it was faffy and there should have been an option to use conventional menus, but there was definitely potential for good there. People talk about innovation and how we need more of it, but if you keep diving on riskier ideas like genestealers with rage virus then of course devs are going to prefer sticking to proven formulas. Aside from that, there's a lot I feel could have been improved on, but I still enjoyed it start to finish. It wasn't as good as Fable: TLC, but if you're going to set your bar that high then you'll spend a lot of time disappointed.
Another one I've recently discovered is Oddworld: Stranger's Wrath. I grabbed the HD re-release in the GoG.com sale and loved the absolute shit out of it. I heard a lot about how it wasn't in the spirit of Oddworld, which after finishing it I can only assume to mean they just wanted 2D Abe games pumped out over and over. I've got a lot of time for the little green guy, but Oddworld is a big place and I liked the different angle they took on it. One of those few games I got to grips with more after making the decision to use controller over keyboard and mouse, helped immensely by the game supporting it. The first half gets a bit repetitive, but a the twist was to die for. Loved it.