I went back to Black Flag this weekend, and I think I have figured out the biggest problem that the series needs to overcome: the lack of replay value. Black Flag - and to a lesser extent, Rogue - is the only game in the series that has it, simply because you can sail around to your heart's content, plundering ships.
I'd also like to see the return of the traversal puzzles from Assassin's Creed II and Brotherhood, and for the developers to get over the habit of including interesting new features - like bomb crafting in Revelations - for one game and then forgetting about it in the next release.