Mentioning Desmond's story is why Assassin's Creed lost.
I found Desmond's story to be interesting until Brotherhood which was less interesting and more weird.
ACI: Introduction to Desmond, don't know anything about him but he's supposed to be you; ok. Captured by mysterious corp with sinister intentions, they turn out to be Templars which was really neat at the time because the Templar / Assassin universe was new. You get to sneak out of your room when nobody is looking to search for clues, try to escape, while ominously hinting that you are going to die at the end of all this. Desmond gets saved by Lucy and then starts seeing all the strange symbols and riddles because he gains Assassin abilities... oh man, sequel! Really limited but since the game was really about Altier I thought it fit really well.
ACII: Desmond escapes from Abstergo with Lucy which is a great start to the game and a new chapter in Desmond's story; he's not a vegetable any longer, he is capable of doing modern day Assassin things himself. He gets plugged into another Animus to train him into a super assassin via Ezio. That was good. Then the story slowed way down until the end where Ezio receives a message for Desmond and you're beating up modern day Templars through the credits (best credits ever).
ACIIBH: Desmond and crew go to Ezio's villa as it is in modern times. An interesting setting, but by now we should begin some resolutions. The story tried to continue the mystery and conspiracy of the first two games and failed to deliver because we already know how the system works and it was time to go do something about it... instead Desmond continued to search for more mysteries through Ezio but the mysteries had become boring. They tried to end it with another cliffhanger but it didn't make sense and felt really contrived.
ACIIREV: Revelation had his dispassionate poetry object puzzle things which gave us a backstory, basically establishing the character in the Templar / Assassin universe which was unnecessary. The whole 'shattered mind' thing felt more like an excuse to keep making Ezio games than to advance Desmond's story. At the end Desmond wakes up. Good, finally! Now with the combined knowledge and skill set of Altier and Ezio we can take out Vidic and the entire Templar structure of command!
ACIII: Nope. More alien mystery stuff. There are a few missions for Desmond, but they feel like tiny snippets of the story that SHOULD have been told. Then they end with what is supposed to be another cliffhanger but I found it profoundly uninteresting. A pointless end to a pointless story arc that magically saves the world.