I think the back/upper-right looks fine; although, you may need to make the space longer for games that incorporate the wiimote. I also don't like the spine. Too cluttered and bundled up. You could try to make it match up with TP
http://www.thecoverproject.net/view.php?game_id=1403
Or take the spine of the GBA version and elongate it a little.
http://www.thecoverproject.net/view.php?game_id=75
In response to the first complaint (about the back/upper-right and the layout of the controller buttons, here is how it currently looks.

This picture shows what it would look like if the Wiimote, Classic and GameCube controller are all supported by a game. As you can see, I made the space somewhat longer so the Wiimote icon can fit in. Also, both controller icons are now no longer on their side.
In response to the second (the complaints about the spine logo - I take it you don't dislike the layout of the spine except for the cropped logo I used):

Picture number two shows off the new game logo. As per SMM's advice, I took the logo from the GBA cover. Didn't bother elongating it, though. This picture has 2 icons (Classic controller and GameCube).
Also new is the Wii Points indicator.
EDIT: Perhaps I could remove the Wii logo from the spine and move the Virtual Console logo to the top. Let me know if that's an idea I should pursue.