Looks like the main problem is price and 1st party lineup.
In all seriousness, the main problem seems to have been the higher price of the Wii U, even accounting for inflation, and the lack of first party games.
Compared to the N64: The Wii U has an okay Mario platformer, which is almost as good as a revolutionary 3D one, but lacked the variety of exclusives like Killer Instinct, Cruisn, and Wave Race at launch. Afterwards, the N64 didn't actually sell that well (probably off of SM64's success mostly) until a price cut to $150 and Mario Kart saved the day. And then, by the time the Wii U got Pikmin 3, the N64 had Goldeneye and Star Fox 64. So that's something like four killer apps for the N64 in the time the Wii U has had one at most.
Compared to the GameCube: This is the most damning comparison to make, but when you look at what the GameCube had, it was impressive in its early days. By August, you had already known major hits like Smash Bros and Super Mario Sunshine, but also new hits like Luigi's Mansion and Pikmin. Not to mention better 3rd party support like Star Wars, Sonic, and Resident Evil. I'm sorry, but the closest thing the Wii U had to a hit in America between launch and Pikmin 3 was Lego City... which has sold only about 230,000 in the USA thus far. And once again, the GameCube had a major price cut pretty early on, which gave it that extra boost towards the end.
Compared to the Wii: This seems almost unfair, but notice how Nintendo had a game every month or two for the Wii in 2007? The exception, March, was a low point for the system. Also note that, thanks to similar specs to the GameCube, devs were easily able to shift gears. Note how soon Mario Party 8 came out, the fact that Super Paper Mario was once meant for the GameCube, and how Metroid Prime 3 used existing assets.
So, what can Nintendo do at this point? Well, by cutting the price by $50 and varying the bundles a bit, they're off to a decent start. Wind Waker HD ought to sell well (see Ocarina 3D on the 3DS), and even if it doesn't reach a million in the US alone, it will move some units. Wii Party U might flop, but it could also end up being this gen's Wii Play, albeit a few months late. That's better than the Wii, GC, or N64 had in October, although the Wii and GC had better Septembers.
Looking into November, Nintendo has a 3D Mario. This is big, especially since it is that newfangled 2D/3D mix that people loved on the 3DS. It could end up being just as big a hit as Galaxy, especially with multiplayer thrown in. This is roughly equivalent to the Wii's Galaxy and the N64's Diddy Kong Racing, and is actually better than the GameCube's equivalent (Metroid Prime).
December is even better for Nintendo. DKCR:TF combined with Wii Fit U ought to, in combination with already released and the above mentioned games, finally make the Wii U a system with a broad library for its target audience. The fact that they're (like SM3DW) recycling resourcesfrom other games is no problem if the Wii was any indicator.
tl;dr Nintendo actually may have made the Wii U TOO powerful, since it created delays for some of their games. Some of the most notable Wii U hits of 2013 are going to use recycled resources, but the Wii proved that this is acceptable. The Wii U has been a failure so far, but redemption is still achievable.
In other words, don't count it out until its third Xmas. ;-p