While this technically isn't a true sequel idea, I'd love to see the entire Marathon trilogy remastered in a modern game engine rather than in a release like AlephOne or the semi-fun nightmare of the XBLA Marathon: Durandal.
I think it would be an interesting way to introduce many gamers to one of Bungie's best games. Additionally, I think that a remastered Marathon Trilogy might pave the way for some other remastered classic games. Just updates without messing with core gameplay or story. Well, maybe some changes to gameplay. Marathon would be a very different game with a true physics engine, and you know, the ability to look all the way up or down. Marathon also has a pretty good story if you like to read.
Marathon would be a good stress test for remastering games that are story-heavy. It's got a ton of story elements, some of which directly reference a good deal of classical material, other's deal with psychology, etc. But it's also a shooter. And the masses love them their shooters. Plus, if it's got the Bungie name on it, it'll sell like a hotcake. Imagine the looks on all the bro-gamer's faces when they pop in the remastered Marathon series expecting Halo.
Sure it could probably be a disaster but what the heck? Marathon's so good that people are still playing it online! Not many when compared to most online gaming circles, but it's still a damn good game with a really engrossing narrative.
Now for straight up sequels? I'd like to see a Mirror's Edge sequel, or maybe an actual sequel to Morrowind. Oblivion is the next game in the Elder Scrolls series, but it's too much classical fantasy stuff. Morrowind just had its own special brand of fantasy that was unique. I'd love to see that in a new game.