Hmm. Good question.
For my own part, I'd like to see Liara and Kaidan/Ashley become playable again (presumably after Liara finishes up her ME2 storyline). Wrex would be nice too, although considering where he is in ME2 he'll probably just turn up as your reinforcements against the Reapers. Add to these whoever survives from your ME2 party, and have this be your playable cast for the third game. It's too late now to break in a bunch of new characters as ME2 did. Granted, depending on the choices made in ME1/2 this could be a big cast (5 of your 6 crewmates from ME, plus a maximum of 12 from ME2 is 18). This could probably be circumvented by DLC over time, however, and since it's probably not going to be released by 2012 they might not have a problem with it by then anyway, since most players who didn't work for the best ending probably lost a few team mates in ME2.
Secondly, I'd like the game to be more balanced then ME2 was in terms of the combat. While you were still blasting your way around the galaxy in the first game, there were plenty of vehicle sections (ignore the God-awful handing of the Mako for a moment) to break up the shooting. The absence of them in ME2 (except for in a couple of DLC's, which I welcomed), means it sometimes feels like you're playing through a bunch of shooting galleries. Keep the combat system of ME2, but throw in more ways to break up the shooting and I'm a happy man.
The only other thing about the combat that I'd like to see is the type of enemy vary more. In ME2 almost all enemies were human or humanoid. This adds to the repetitiveness of the shooting as I said above. In the original ME this was present as well, but not to the same degree. When I was running around Noveria and the bugs started coming up through the floor I thought I'd walked into an episode of Starship Troopers. The galaxy's a big place, and presumably all its life doesn't walk on two legs.
In terms of the character's powers, I'm happy with the ME2 system of having a few, powerful ranks for each skill. It could be improved by having more skills per character, though (even just one or two more), and more diversity in the skill sets of each character instead of several having access to Throw, Concussive Shot, etc. I realise in the light of the cast I want this is probably difficult to do, so I don't mind some skill duplication if it means I have the team I've built up over the past two games.
Resource mining didn't bug me as much as it seems to have done a lot of people, but I accept a better system should be found. Maybe if they use the Firewalker from ME2 to actually run around a planet for resources?
Finally, the plot. I agree with the original poster that having a wide range of endings is crucial, as well as tying up the loose ends that remain. This is apparantly the end of the series, so the ending must be satisfying. That being said, however, I really wouldn't mind a kind of "bad" ending where, if you screw up, the Reapers actually win and wipe out all life in the galaxy again. Knowing that you could fail in more ways then just having Shepard killed and respawn adds a good degree of tension. This is basically just an extension of the worst ending of ME2, but it was a good idea, so why not?
A long list, I know, but most of it seems realistic.