If you like Assassin's Creed and don't like Desmond, I pity you. When AC1 got tedious, I kept playing to learn more about Desmond's story. AC2's animus story was much more engaging, but I still loved every single bit that I learned about the Modern Day times of Assassin's Creed. From what I've seen about people complaining, they see Desmond as a glorified framing device. If you want to enjoy the modern portion of the story, cut that shit out. Stop looking at stories so technically. Sure, Desmond is a way to hop between different times, but if you look at ANY element of ANY story that cynically and coldly, you will hate it.
Treat it like part of the story. Dig through all the emails in all the games. Trigger all the conversations with lucy and shaun and rebecca. Trawl through all the glyph puzzles, and begin to see the depths of the centuries-old conspiracy, and the implications it has on all of history. Jesus, aided by a peice of eden taking the form of a travellers hood. Moses, wielding the Staff of Eden. George Bush, a Templar lackey. Hitler, faked his death only to be taken out by an enterprising assassin and have his apple stolen. Edison, conspiring with hitler and other templars the start the war in the first place.
The futuristic, sprawling conspiracy is the best part of AC's story. It can make up for even a lackluster Ezio story like Brotherhood, with the glyphs in that game which told the story of how the Templars engineered systems of control and how the people fought back over the years.
No-one's ever enjoyed a story they went through with one eyebrow raised.