Man, they worked seriously well with the footage. I think that Yoda's appearance was addd in as an afterthought, because the footage shows Neo looking in 3 different directions. He had to add someone to his left because he kept looking there. So...he picked footage of Yoda because it matched the camera angles...and the height of Neo's gaze.
Don't be too harsh on him, he had to have done a LOT of work to splice that together, it was really impressive...