I find that Ezio is probably the most developed Assassin that we play as, we stick with him for several decades of his life after all, and that leads to us getting a lot more insight into his character. He's funny, charming, good-natured, and kind of cynical; he's a very enjoyable character through and through, even with his Inigo Montoya-esque starting motivation. He get's my top pick.
After that, I have to say that Altair is probably the best. Revelations really helps rehabilitate his image and personality, it made him a far more enjoyable character, and even gave him some levity in his dialogue. Plus, his Revelations voice is just awesome, and he also has by far the coolest outfit out of any of the three main Assassins.
Connor is....well he's not a bad character by any stretch of the imagination, but I don't quite like him, for two main reasons. First off, he's just so self-assured and self-righteous at times that it can be a bit off-putting. He's probably the only Assassin of the three that never seriously questions some aspect of the Assassin lifestyle, he just mainly accepts it rather quickly. the second reason is perhaps a bit pettier, but nonetheless important to me: Connor could really stand to lighten up on occasion. I know that he's more stoic and serious than his predecessor, but even still he could stand to have at least a little fun. Humor, to me, helps make a character relatable, so that's why I'd put this as Connor's problem.
As an honorable mention, though, I think that we can't exclude Giovanni Auditore or Haytham Kenway.
I'd put Giovanni, based on what we saw of him in Lineage, at about Altiar's level of coolness, as he has the whole "double life" aspect to his character and Ezio had to get his tendencies from someone.
Haytham, on the other had, I feel really gives Ezio a run for his money as most interesting character in the series. If he had more time as the player character, and didn't undergo such a shift in characterization during the timeskip, I think he'd really be just as interesting as Ezio. Seriously, he's got an awesome story arc (in the beginning, anyways), and awesome accent, and an awesome outfit (the most non-Assassin one of the bunch, I really liked it). I think it would be great if we got more time to play as him in the story.
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I have to ask, though, has anyone played Liberation yet? I haven't, but I want to know what people think of Aveline, as from what I gathered, she seems like another very compelling character.