As much as people hate Altair, at least I believed in him as a character. He had an arc, grew as a character. I like how it started out as a jaded asshole and then realizes he's got a lot to learn about everything. Ezio, as likable as he is, is kind of generic. A genuinely inoffensive, rogueish character who gets some tragedy thrown at him and spends the majority of the series saying "Bene, I will do this." He's a confident Desmond.
And the way the (historical) conflict was presented overall in AC1 was much more gray than anything that has come after. Templars had believable (if twisted) world views that they truly believed in. The Assassins weren't always the heroic protectors of goodness and freedom.
Every other villain from there AC1 on out out is a mustache-twirling bad guy who craves TEH POWAH. When guys told me why they did what they did during their confessions in AC1, I'd actually stop and go "Huh. Yeah, I can kinda understand even if I don't agree. But you're still dead." Ever since then every confession is "FU Assassin!" or "I'm such a wussy and now I die." None of the bad guys in Assassin's Creed games now have a reason for what they do other than guys in the previous games did it. The writing is completely Hollywood now. The info blurbs allude to the fact the "good guys" aren't necessarily good, but none of that comes across in the rest of the game.
If AC1 had AC:Brotherhood's mechanics and design, I'd consider it the best of the series. As it is, what I like about AC is spread out over all the games, with none of them hitting all the high notes, and my love of the aesthetics being the one thing that takes me from game to game.