And for the record, I think it's not that people don't like Connor. I think it's just that he's nothing like Ezio (who had three entire games... well... two and a half games ((looking at you Revelations))to develop).
I think we'd honestly be hearing more complaints about Connor if he was more like Ezio or Altair though. He's in a no-win situation. Personally I love all the Assassins so far, and precisely because they are so varied in motivation, action, and even thought process.
And about Desmond... yeah... most of his stuff in 3 seemed to be almost rushed. Like they spent so much time on the Animus stuff that they almost forgot Desmond had to be in it as well, and had to just make up stuff fast to catch a deadline. And his ending... well it made sense, and it sucked. I've said it before but I get the feeling that the ending was probably written by the time Assassin's Creed 2 was finished, but it was changed between Revelations and 3 in order to find the easiest way to continue Assassin's Creed as a franchise.
And actually, since I'm feeling like typing more, I have minor problems with each of the Assassins.
Altair: Was a bit of a fanatic for most of his life. He followed al-Mualim completely blindly... which is odd considering how much the Assassins value free thinking. But that's the arrogance of youth. And it's actually pretty historically accurate with the real Masyaf Hashhashins.
Ezio: Took way too bloody long and spent way too little time thinking for himself to be Mentor. But that said, I'm pretty sure he was the best guy for the job around that time. (Again I love Ezio, but he really did spend most of his time just believing anyone with a branded finger instantly, and never seemed to realize the Templars as a whole weren't mustache twirlers. Just the Borgias)
Connor: If he would have murdered his father the moment he had the chance he could have probably forced a small alliance with the Templars with the remaining members at that point. That and he seems to view the brotherhood as more a means to an end than a way of life.
I tried to play this as my first AC game, and I just didn't like it. The story is so unappealing to me, and it just seems like they want to throw you through a gauntlet of historical figures. Connors character is lame in my opinion, and he's too much of a stereotypical "white man took my land now they will pay" native american. It's like they forgot to convey the fact that he did have englishman blood in him. I understand that he was raised by his mother and all, but jeesh. Everything else is cool and all. The gameplay was fun, but it was more or less the separation of the story that killed it for me. I don't appreciate the over-story of Desmond like a lot of you AC vets probably do.