I think what most failed to understand was that it's suppose to be viewed as 1 singular movie, not 3 different ones.
If you look at any movie....The beginning is rich in story, you are learning the most about the characters and how they think, behave, and get introduced to the main conflicts. The middle is action, with bits and pieces of the story peeled away. The end third is the resolution of the conflict
Breaking the movie up into 3 parts shows this. The first clearly had the best story, the 2nd had the best action, and the 3rd was the conflict resolution.
Granted it was difficult to understand, I find myself learning something new and different every time I watch.
As for what a 4th and 5th installment could be. I personally wouldn't mind seeing the story of Morpheus and how he came to his enlightenment. I believe he said there was another (assumed) previous generation "neo" that freed the first of them. Now was this in a previous version of the matrix or in fact the current one who knows. There are many ways they could go with it, and I trust they would write something that would appease the die hards.