I think the biggest problem Nintendo has faced with the Wii U was a lack of direction. The system is basically a Wii with a better processor/graphics, and then this add on controller that nobody knows what to do with. The idea of having 1 controller be different than the other 4 was a bad move.
They were also lacking clear direction on launch. The biggest titles for Nintendo have always been Mario & Zelda. With the Wii U I have no idea what the "flagship" mario game is supposed to be, Super Luigi Bros/Super Mario 3D Land? Are they just a bunch of secondary knockoffs? Zelda didn't even get it's own release yet. Windwaker HD is coming out, but it's a revamp of an old game, and it took how long to even make the announcement?
I also agree that Nintendo needs to develop new properties besides Mario & Zelda, but both of these should have had clear release announcements before the console release.
The innovation was lacking for this console, and the upgrades don't quite seem to justify a new console (yes 1080p is cool, but graphics have never been the driving force for nintendo games)