If that would translate into more support from SE and a better relation with Nintendo as a whole, I say go for it. After EAD finishes with Zelda U, go work with Square. I don't see the problem. Even as a spinoff, just the names of the developers alone would sell the title. Also, there's no reason to think the game would be bad, neither SE nor Nintendo would allow the game to be bad.
One Zelda game in exchange of SE full support for a gen, seems reasonable if they can pull it off.










