I really liked how the trilogy played out.
In part one we were introduced to the Matrix and all the ramifications that go along with a "fake" world. It was more personal and character driven.
In part two we see how powerful "The One" is as he can basically do anything inside the Matrix. The story becomes more epic as we are introduced to Zion and the Architect. But, Neo still doesn't know what he is supposed to do. The Architect tells him what to do, but Neo makes a choice not to do it. The movie also ends with the the possibility that the prophecy is a lie.
In Revolutions, Neo chooses what he has to do to save mankind. He becomes a Martyr by bargaining with the machines. His life for humanity - Smith's destruction to save the machines. He fulfills the prophecy even though the Architect said it was a lie in Reloaded. So all along Morpheous was on the right path and choice turned out to be a huge component of it. Something the machines didn't understand.
Kind of long but......
