I was over on Giant Bomb and they had a thread about "Favorite Flawed Games." I really liked what I wrote about it so I wanted to put my response here.
You can check out the thread here - Giant Bomb Thread
I can think of a few games as I usually find myself enjoying the "flawed" games over the triple A super polished ones.
Far Cry 2 is probably the top of my list. With everything it got right the flaws are still present. Guard post respawns, broken stealth and for me at least the lack of co-op in a game that is just screaming for it. I can't think of another game recently that was just begging to have co-op. So many things are already there that make you wish you could play with someone else, it's like Ubisoft was teasing us with them. Instead of tacking on a competitive multiplayer they should of taken that time and effort and made co-op.
Next one I think of is Stalker: Clear Sky, that game is still buggy as hell. The first time I tried to play it I got stuck in an endless death loop because the game decided to kill me as I saved and I have no idea why. It wasn't radiation or an enemy attacking I was standing in an open field and just dropped as soon as the save did it's thing. I finally ended up using Clear Sky: Complete to play through it and then even ran into that Limansk crash bug. While I think Shadow of Chernobyl is the superior Stalker game when I was done with Clear Sky I had really enjoyed playing it and would consider giving it another go when it's time for me to replay a Stalker game.
I saw a lot of mentions of Too Human on here and while I don't really think that game is "flawed" in the since of it being broken it just didn't live up to the hype. Me, I absolutely loved it, I spent 60 something hours playing the living hell out of it until I found or traded for all the Elite armor pieces. I think at its core Too Human was a good attempt to bring a Diablo type loot gathering games to consoles, I liked the analog stick combat and the overall feel of the game. I just think when people hate on this one it's that they were expecting a game as unbelievably amazing as Diablo 2 and what we got was just a pretty good game.
A game I didn't see mentioned here yet is the newest Turok. While not the same Turok we know and love from the N64 days I still thought it was a fun simple FPS game. Every shooter we get doesn't have to be super military Call of Duty like shooter. Turok was like a throwback to the FPS games from back in the 90's and that was the main reason I loved it.
I guess the last game I want to mention is Cryostasis and really for the following reason. When I got to around level 12 the game would constantly crash on me until I messed with settings and worked through it. I've never had a game work better for me after I've turned the settings UP. Besides that another brilliant game more people should get a chance to play.