The truth probably is, that at the time they allegedly came to Nintendo with this exclusive idea, Nintendo was still riding high on success, and the Wii U wasn't even close to launching, and they perhaps just didn't think that they needed to make a deal like that. In hindsight, obviously, I would imagine given a second chance, they would absolutely go for it.
Then again, it's not as if a kid/family franchise like Skylanders, regardless of how popular it is, would help Wii U THAT much. It would help, don't get me wrong. It would likely get more families to buy Wii Us, and more kids to want one. BUT, it wouldn't change the overall landscape Wii U currently has, and certainly wouldn't change the minds of any of the so-called "hard core" that are just too hard to ever buy one.