I would want something like custom weapons, like new ones that are modded into the game, even if it's just singleplayer. Also maybe some real life advertisemants, I wouldn't mind seeing a few Geico ads at the bustops. I'm not sure how the texture coloring works, but if it's possible, modding the alien accents from red all to blue would certainly be interesting, maybe make Crysis 2 look like almost a different game. And of course, custom levels with more vehicles, I really want to drive some taxis around, maybe some helicopters too.
this all depends on how moddable the game will be, and I hope we will be allowed to mod singleplayer into Crysis 3 or equivalent.