I agree with you to some extent. I have to disagree with Desmond's memory sequences however. The first person puzzle simulation seems to be a bit frustrating in my end. Though I finished them all, I can't shake the bad taste it has left behind in my mouth. The fact that we got to learn more about Desmond is great, just minus the irrelevant FPS puzzle and you got yourself a masterpiece. Playable flashbacks would have been better imo.
And multiplayer...well all of the above is all I got to say. Multiplayer specific achievements, unbalanced progression system, online passes and the lack of players easily breaks this game for me.