Is it really that convoluted?
And I think they've done a good job of juggling two different narratives at once, while telling us this rich story of Ezio and Demond's ordeal on the flip side.
I really like the animus, as a plot device to explain away things that gamers would ultimately complain about. The animus serves it's purpose very well, I think.
It explains away Ezio and Altaïr speaking english, the HUD, subtitles...and everything else that gets seen as a negative because they're too "gamey".