1. It didn't, the story was about the journey of Christ, with Neo serving as an allegory.
2. The movie was meaningful. There are numerous layers to the Matrix movies, and different people discovered different parts of them. Although many people hated the way it ended, it was the only way for it to end, in order to complete the story of Christ. Many people wanted a happy ending, where Neo kicked Smith's a**, but that would have been untrue to the meaning of these movies. When Jesus was on the cross, he didn't use his miraculous powers to fight back, he gave in and died in order to save mankind, or in Neo's case, to end the war between man and machine, and to save Zion.
Neo: Fly into the upper atmosphere instead.
Trinity: This is a *hovercraft*. Not an airplane.
Neo: Who are you going to trust? Sir Isaac Newton or me? Point this thing up.