I'm disappointed Alpha Protocol won't get a sequel. The game had more than it's fair share of flaws, but it also did something new and different. I liked the consequence system it used, I liked that there were so many ways to play the game and it was easy to miss meeting certain characters and such. I liked the frame narrative (something Dragon Age 2 will The be using). The side characters were interesting even if Thorton's VA could've used some work.
It would've been interesting to see what Obsidian could do for the next game. They've never been good at releasing non-buggy games, but their stories are always interesting.
Another one I'd like to see is a sequel to Jade Empire. I know it was never as popular as KOTOR or NWN or the later Mass Effect and Dragon Age, but it was still a damn good game. It had a unique setting, great characters, fun combat, the works. I love this game and still play it sporadically. I know a bunch of the designers really liked it too. I just wish the execs liked it enough to greenlight a sequel.