If you are thinking of heading in that direction: The Architect looks like someone gave him a goose, and the shot on the back cover isn't even in my edit.
Besides that.... 
I know I know you were just fooling around.
I like the code on the black background motif, if it could be done, it would be cool if it looked like the Matrix-breaking-down code we see in the last film.
I am going to give some thought if any particular images jump out as being definitive of this edit. Maybe a photoshop composite of Smith with the original Oracle in a scene from the Matrix 2? Man that would have been great if I could have actually pulled it off in the film. I suppose it would be misleading though.
Are you thinking a single cover art for a 2 DVD case or 2 separate covers?
Definitely wait to you see it before going seriously into the cover design. I don't know how long that air mail is going to take.