You missed the significance of the little girl. She's important to the story because, remember, she was there at the end talking to the Oracle after the Architect. I've read somewhere that she was the result of the machine's discovering love and she was given power to create the next Matrix. Notice that the little girl runs up to the Oracle at the end and points at the beautiful sun rise. The Oracle asks Did you do that? and the little girl nods her head and says For Neo. She created the sun rise with love for Neo.