Just have to say, Assassin's Creed 2's story is incredibly flawed for a number of reasons. First, the whole format of using the Animus is terrible, because it poses fundamental questions about the "real world" setting that will never be answered. Like, what year does this take place in? What is the underlying purpose of creating this Animus technology?
If you compare this to say nanomachines in Metal Gear---a lot of the plot elements using nanomachines are really rediculous (ie, Liquid Ocelot's talking arm, remote control of an entire army), but at least the concept of nanomachines is a logical extension of military technology. Its a device to warn us of the perils of war and technology---something Ray Bradbury or George Orwell would be into.
The Animus has no logical purpose for existing, other than that there is some MacGuffin in the plot having to do with finding details from peoples' memories in historical periods. Its sort of like if all the Harry Potter books were about the Pensieve, but we never even learned like what magic was, about Hogwarts, or anything about trying to find Voldemort's Horcruxes.
That said it is impossible to become involved with any of the characters in the AC history segments, because we have no clue what the relevance of these Assassins' memories is. If you block out the segments of the game involving the animus then the story is just a poorly written, cheesy adventure.
Ezio isn't a good character. I mean there is nothing to him. He's just a generic guy with an Italian accent. And like, the games' do things like put Leonardo DaVinci in---but the point isn't to make him a character---its to say "look, how novel! a historical figure from history in your video game!" I mean, to me, at best Assassin's Creed's stories are something akin to old cartoons like The Magic School Bus, or where some kid time travels with a talking animal to learn about history.
What I'm getting at is there's this really important distinction arising maybe across multiple mediums---but in video games especially---between actual story telling, and franchise construction through layered meta devices, and lore. In AC the Animus doesn't really serve a purpose except to raise questions about the universe itself.