A sequel would be really nice, I'm loving this game, though I do hope they don't listen to too many of the complaints about the game, some of them (from reviewers) have been damn right stupid. Some reviewer wrote "It's not fun to have maths dictate wether or not I hit something, that's not fun!" wich is a downright foolish remark when reviewing a RPG. Please, please don't go the ME2 road!
I would'nt mind this at all, but at the same time I'd prefer them to keep it simple, possibly more missions/locations aswell. Building an interesting city would take them alot of time and resources I reckon, possibly too much. I do like the idea of more social "mingling" missions and wiretaps though.
Don't think they need to overdo it though, what with toiletbreaks and all. But they should impove it, no doubt about that, and perhaps have some more random patrols on higher difficulties aswell. AI reacting to dark and light areas in the same way as the Thief games perhaps?
I would prefer if you had some amount of control of your assistance, instead of them going in on their own, coordinating your attacks so to speak.
I myself don't mind terribly if they keep things simple here, it's more important to balance the allready existing skills better than they are, and polishing it up a bit better. Better menu's, perhaps adding a few more looks to the mods of your weapons (I.e. reflex/laser-sights and scopes looking the part, and not as a scope with a reflex sight)
I would'nt mind if they use the existing engine as is, with just a few bugfixes - I just want to have another game like this one. Not for them to make an "Beta Protocol" that is to Alpha as ME2 is to ME1.