I just finished this one and liked it alot. Let me just say one thing, I think the writing on this and Modern Warfare 2 both sucked ass. I do love the story of Assassin's Creed, especially AC2 but there were alot of times in the game when I was struggling to understand what was going on. For example, the prophet idea. That totally came out of no where. Firstly the Spaniard said that he was the prophet and I thought to myself, wait a second, what prophet?' Then by the end when it became obvious that Ezio was the prophet who would carry the message for Desmond it made sense but it wasn't properly explained. There are a few other examples from earlier in the game too when things were just not fully developed or introduced properly. Nitpicking I know but I feel that good writing is essential towards creating an epic game like Halo or Mass Effect.
i hear ya. even though i thought the gameplay and everything was awesome i too felt like i was lost a lot of the time with the story. i just played through it. reminds me a lot like metal gear, for most those games i had no idea what they were talking about lol