Rambling personal experience.
I really love 80% of Assassin's Creed 1. But I honestly just wanted to get out into the world and do my thing and so I found the constant trips back to the present day and the meandering conversations with Al Mualim to be blocks to my enjoyment. I can see what they're going for, but Assassin's Creed 1 feels way too eager to force its plot down your throat and combined with the rather limited game mechanics means that it often feels like any pleasure derived from the game is almost accidental.
Which is a shame as the setting is fantastic and the villains are great. As much as I love the Ezio games the villains never felt as immediate or as threatening as the Templars from the original. Assassin's Creed 1 really feels like a game where the assassins are on the precipice of destruction, whilst the Ezio games make the Templars a far less impressive threat. By Revelations they're practically scrabbling for resources. I also think there's a purity to the gameplay of Assassin's Creed 1, your limited move set and tool set kind of forcing you to take less risks. There are moments in the game which are just amazing, riding across the Holy Land at sun rise, climing the cathedral in Acre, engaging a host of about 30 crusaders about Damascus, which are some of my all time favourite gaming moments and none of them have anything to do with the claustrophobically structured main game.
Then again as much as I like Assassin's Creed 1, I love Assassin's Creed 2 for taking on the criticisms that people had for the original and actually addressing them. It's a real rarity to see developers actually respond to critical and fan reaction and do something about the criticisms. As such even though Brotherhood and Revelations refined the formula, I still view #2 as the series crowning achievement.