The Assassin's Creed movie will undoubtedly come out after Assassin's Creed III is released. Hell, it'll likely be released after whatever spin-off or semi-sequel Ubisoft has planned for 2013, too. This means that, at the time it's being made, there will be at least six full Assassin's Creed games to pull content from, as well as a smattering of animated movies, comics, and books.
Because of this, the writers of the film won't need to rely too heavily on trying to replicate the events of one game or one part of a story. They could pull from whichever sections they want, or even attempt to make the movie span the time of several games. If they wanted to play it almost like a time-travel movie (yeah, we know the Aniumus isn't actually time-travel, but work with us), they could do that, too. Just imagine a thrilling action film that pulls the viewer through 1100s Jerusalem, 1400s Rome, and 1700s America – it'd be amazing.