I was never a fan of the modern-day sections of the games, but any hope I had that they would at least make sense was lost when they killed off Kristen Bell's character in Brotherhood because she wanted more money. They turned it into a big cliffhanger and had people speculating for over a year, then they revealed that she was a triple agent that had been working for the Templars all along in some crappy DLC for Revelations. With AC3, they had set the stakes so high that there was no way they were going to finish it in a satisfying way, so I wasn't surprised when I discovered that the way to save the world was to have Desmond press a magical button and randomly die.
I know that some people like the sci-fi element of the games, but I'd rather they just dumped it entirely. I play the AC games for the open world free-running in historical locations, not some crappy sci-fi meta story.