What a lot of people don't realize is that Neo was only ever just a means to an end, and he along w the rest of humanity were not the main characters of the story. The Machines/Programs and their emotional evolution, is the ultimate plot. This is why in the last scene all humans are absent and you're left with The Architect, Oracle and Sati. It's about their ability to develop acceptance, hope, and love.
7:09 this shot is so just epic. the neos in the screens behind neo all making the same choice and the neos in the screens inside the screens are all doing the same. i aspire to have that determination