I think it's time to take the AC series in a new direction. Not sure what that direction would be, but pirates is pretty much a variation of the same direction.
Maybe they should play more on the whole "building the brotherhood" idea. Like have a game where you actually go out and recruit assassins like in the other ones, only this time make the recruiting process much more entailed. Like give the people you recruit special characteristics (some are fast, some are strong, some can climb fast, etc) then actually play as the assassins you develop as they go out on missions.
Or maybe they should just start considering the idea of moving the assassin thing up to the present, or the future.