I know I'm a little late to the conversation here, but I figured I should share my views on the differences between the two main AC games. (Lol, I had trouble finding it because it was in a sales thread. Insane!)
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Here are the areas where I believe the original Assassin's Creed was better than the sequel:
Story - Considering how much more involved the ACII story was supposed to be, it was odd how disconnected I felt from it all compared to AC's story. They try to toss you straight into Ezio's life, but it just doesn't seem to work out. Instead, you end up feeling more for Altair due to all of the dialogue between him and his master/contracts.
Combat - Sure, there were a ton more combat options in ACII, but it was almost impossible to get together a group of more than 6 people at a time. It just felt boring because the combat was over before it got a chance to begin. I loved running into a group of ten or twelve baddies in the original and completely destroying them using only hidden blade counters.
Art Style - I didn't really like the stylized look the characters and environments had in the sequel. Something about the "realistic" tone of the first game appealed to me. It was nice and gritty while Italy was way too clean.
Assassination Contracts - Altair didn't have a "personal" reason to kill his targets like Ezio did, but he seemed to connect to them more. Also, the targets really had a personality to them in the first game that made you want to kill them. For example, that Priest Doctor was experimenting on the beggars of the city. Cruel bastard. Every single one of the targets in AC had a unique personality. In ACII, they all just felt like random fodder.
Desmond Segments - I preferred the stealth aspect of these in the first game. It was fun sneaking around and decoding emails and the like. Doing the same thing I was doing in the past in the present but with less abilities was boring in ACII.
Mission Structure - I sorta liked the hub-like nature of the first game. The GTA-style missions in the second just felt stale.
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Of course, there are a few things that ACII does better:
Character Design - Ezio has a far more interesting design than Altair.
Actual Missions - So much more variety here. Really cut down on the repetitive nature of the first.
Setting - Italy just appealed to me more.
Miscellaneous Stuff - Building up Monteriggioni, looking for treasure (even though the rewards were pretty stupid), the ability to dye your clothing, upgrading armor and weapons, and the sheer number of weapon types you end up with were all amazing parts of the game.
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Now, I may not have gone much into some of the ACII stuff, but I really do believe that it improved upon the formula in a lot of good ways. I just think it took a step backwards in some.