Its a combination storm of reasons.
At the center of the Wii U storm is the fact that no matter how Nintendo try to paint it, the system specs are not up to par of what expected from a home console in the 21 century. The original Xbox set the bar of where consoles would be going, and unfortunately, Nintendo have failed to learn and emulate it (four controllers was good). Now, some will say that specs don't matter (they might not to some gamers personally) but to game developers who have to actually create and sell games, they matter a hell of a lot. This will differ from one dev to another for their own reasons.
The apathy coming from third party devs/pubs is partly because the high end tools they use to create games are always progressing forward. And when Nintendo create a system like Wii U with static/back peddling tech in todays market, it shatters their confidence as to what they can create on it and ties creative hands. A developer or publisher, like anyone in a technical field, can usually weigh up the specs of a system, and know whether their big games can run on it or not with grief or not. By doing so they know whether to invest in Wii U or not. As you can see, many of them aren't doing so.
When Nintendo first showed Wii U at E3, they didn't want to give out the specs as is normally done. This raised eyebrows naturally. You wouldn't go to the Moon based on dodgy math, would you? Specs and measurements matter, whether you are baking a cake, going to the moon or creating a games console other have to make and sell their wares on.
When I first saw Nintendo wheel out Wii U, it spelled a flop to me. They had a tablet controller that they had no idea how to use effectively to justify its existence, seeming kind of tacked on to look progressive and you only get one of them. While Nintendo were acknowledging the rise of tablets and phone games, the Wii U wasn't going to really cut the mustard for the various kinds of games we play these days. On top of that, it still did not have a standard hard drive, one of the most key parts of a modern games console, that many devs rely on to create their games. So its another Nintendo console third parties mostly opt out of, following Wii and N64.
Lack of third party games, means lack of Wii U buyers and users. Devs/pubs need high numbers of Wii U users to justify creating games for it. Without those numbers, its a risky gamble that might not pay off. And thus, 90% of the big ticket games Wii U misses out on. That's a rough number that's not going to improve, with two big heavyweight console launching soon. Wii U will naturally get a few sweet games here and there as any system does, but those games will never be enough to save it from the scythe looming over it, as each month its Wii U sales numbers are terrible. High price of games and systems doesn't help the situation either.
I'm afraid Wii U's a flop of a system, that's a fact. Nintendo will paint a positive stubborn face like they've done many years before with previous gens, refusing to drop its price etc (seen it all before) but I don't think even a price drop will save it when games are still few. Its not enough to kill the Nintendo 8 billion dollar beast, so despite its flopping we'll have to wait and see what Nintendo plan post Wii U. Feel free to enjoy it, if you have one, mind.
My guess is they'll put more focus on handhelds, and maybe leave home consoles alone for a few years, til they can regroup, rethink better and get that act together again. They will be back (I don't expect we'll see a Wii U successor until 2015/16), but by the time they return will they really have learned anything or just repeat the same home console fails again?
