AC1 is still the best in the series for this reason. The problem with the story in AC2 is that it was basically a process of meandering dot connecting. "Go to A, then go to B, then go to C." But AC1 had a much more organic and open plot structure. "Kill A, but do so by doing any number of tasks 1-6, then plan your attack using that information in any way you like. Then move on to kill B." Only in the final area did AC2 trust players enough to re-introduce this structure from AC1.
Brotherhood and Revelations were about trying to combine the best of both worlds. And from a structural perspective, I think they both succeeded. Of course, Revelations suffered from a massively under-developed story in general, but that's a different issue.
Ezio is just a typical video game hero. Altair was unusual. He was much more of a genuine enigma than most game characters, and the game was never about him. It was about his place in history, and his role in the "underbelly" of that history. God, I love that game. Just talking about it makes me want to play it again (for the fourth time).
I completely disagree. AC2 appeals to the instant gratification crowd. AC1 appeals to patient gamers. Unfortunately for us patient gamers, there aren't many games designed for gamers like us. Most of the patient gamers stick to things like fighting games, strategy games, racing games, and shmups. But AC1 was one of the rare games (along with Demon's Souls) that rewards dedication, experimentation, and patience. But you really had to be willing to push the boundaries of the game and not assume that it would all just be handed to you on a platter (as it was in AC2). Playing without the minimap or main map went a long way toward taking away the handholding and presenting the game on its own raw terms.
Like Irish says, AC2 definitely improved on the mechanics. But it also took the "thinking" out of the game's structure. It does all the thinking for you. Luckily, Brotherhood and Revelations found ways to reintroduce the "thinking" parts of AC1 and continued to refine the core mechanics. If not for the skeletal storyline in Revelations, it would easily be the best in the series. Its mechanics and systems design were absolutely brilliant.
It really makes me sad that AC3 tosses all of that thoughtful iteration and refinement out the window.