Sega's said they aren't going to permit a sequel, so bringing anything from old game into new isn't going to happen unless Sega changes their mind, which I imagine is unlikely. I said in another post though I'd like to see them do another espionage RP.
Now, in a hypothetical world where an AP II was going to happen, I think if Thorton's going to be the MC, he should probably stay male for story/character consistency. If it was going to be a new MC, I'd absolutely want either a female MC or the ability to choose your gender (same if there was a new spy RPG made in a new IP).
It would be hard to do an AP sequel come to think of it, though -- there are SO many people who can end up dead by the end, it would be hard to have a game that accounted and adjusted for all possibilities and still allowed characters to return and have meaningful contributions to the story. In fact, I have trouble thinking of a character who would be guaranteed to be alive in all scenarios... maybe Heck? That's... kind of sad he's the only one guaranteed to live. OTOH, I'd love to see a game where you're, say, an agent for G22, they seemed like a really cool organization.
For any spy RPG, car chases and the like could be cool if the mechanics were well designed, but I'd rather the focus be on improving the existing combat mechanics. Like, for example, being able to actually aim a sniper rifle with the PC controls without spending an hour fighting mouse sensitivity while lining up the shot. Or like having two different command keys for throwing a grenade and attaching one to an area to set up a trap, so you aren't constantly accidentally doing one when trying to accomplish the other. And I agree about having the sniper rifle be opened up as another option for a weapon you could carry, or at least have it be more frequently available. I also want to be able to switch appropriate weapons between burst and single fire as needed.
But the more I think of it, if there were another game using Alpha Protocol IP, what I'd really want is a prequel where you play SIE spreading machine gun fire all over the world.