If Ubisoft is smart, and hopefully they will be, they'll be constructing a completely unrelated assassin in a completely different time period for Fassbender to play. One thing that video game movies struggle with is cleaving too closely to video game narratives and video game characterization, and hopefully, they are going to try to break away from that a bit. I suspect that Fassbender's producer credit is due to his input in constructing his particular assassin and what sort of Templars he'll be fighting. The worldbuilding in the games is ridiculous enough to support this idea.
Ubisoft is probably also excited by this idea, because it means that they can construct a brand new gamearound whatever they come up with (and hey, maybe they can even get him to voice is character! Sweet, sweet synergy!). They're really into the idea of releasing a new game every year, and developing each new character and time period seems like it's a huge undertaking. This gives them two for the price of one.
(Though, if they do cast him as Altair or Ezio, I will totally get my displeased face on. Seriously, people. What the fuck is this and why do we have to keep doing it. WHITEWASHING IS HORSESHIT AND YOU SHOULD STOP, KTHNX.)
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