The weapon variety of Mass Effect 2, but the moddability of Mass Effect 1. I don't want only 4 weapons which feel very boring and all do the same thing, the only difference being a Roman numeral being appended on the end and all of that being redundant when you unlock Master Gear. At the same time, ME2's ammo powers were somewhat "realistic" taking time to switch out, but nobody liked it and the fact that a recent power use meant you couldn't switch was pretty silly.
The weapon upgrades in ME2 were just a different way of doing the whole "numbered weapons" schtick without clogging your inventory, so I don't particularly care if that stays. I also like how money has a little more impact, in ME1 you could get to 9999999 and stay there.
For the different classes, I'm not sure how they should progress. In ME1, there were 3 specialist and 3 multi-classes, but in ME2 each one felt fairly unique (Vanguard and Infiltrator were my favorites for both). I'm not really fussed which approach they take, but I would like to see some less combat heavy aspects of classes being brought forward, as well as that approach in the levels.
Story wise, ME2 is the middle child and there isn't much you can do about that, hence the emphasis on characters. Hopefully, ME3 brings back some more worldly and political interaction with the different species as well as introducing some more delicious conflict. So you're a paragon, but how are you going to get all of your new friends to love each other? Well, aside from choosing all of the paragon options for the whole game and just picking blue dialogue >_>. Oh, and a few more NEUTRAL choices, like Heretic Geth, Krogan Genophage data or Overlord Project, without the Paragon vs. Renegade stickers on each choice.
Also, less corridor shooting, an actual persuade skill like ME1 (although that still was dependent on paragon renegade somewhat), no planet scanning (obvious), armor, a sense of exploration and ACTUAL CONSEQUENCES. I'm sure all of that has been said before.