They bit off more than they could chew, and it got downright pretentious and silly. The Architect stuff, rogue programs, keys, etc, none of that stuff existed in the first movie and so it seemed like it has just been thrust in at the last second. It never felt natural or right. If the Matrix was truly so powerful, then it would have everything in it under total control. Finding out that there are actually loads of rogue programs outside its control, some of them with powers seemingly beyond even Agents, weakened the whole concept and significance of the Matrix. Then there was all of that stuff about Fate that felt like it was just thrust in as philosophical padding for the movie, etc.

The relationship between Neo and Smith was among the best. Neo as a human with a nearly robotic lack of emotions. Smith a machine with nearly human emotions of rage and hatred. One a being of infinite power, the other a being with infinite copies of himself. These are cool concepts in my opinion, which is why it was disappointing when Smith was fighting Neo as an equal, or perhaps even winning at the end of the 3rd movie. The only way their relationship makes sense to me is if he's weaker than Neo, and makes up for it with his numbers. Oh yeah, and the Architect stuff sucks. That can't be stated enough.

But really, even the ending of the first movie, where Neo flies off into the sky instead of the movie ending about half a minute sooner, shows that the writers had little idea what to do with a fully powered up "the One." Underdog rising to become a great hero is a pretty standard plot, and basically what the first movie was, so it's no wonder it turned out great. But the next two just meandered, with poor pacing and lots of pointless elements like Neo at the train station, or really protracted Zion scenes and Zion characters no one cared about.