I think it's caused by all the legitimate complaints you listed in your second paragraph. topped with a failure to keep up with current technology standards which has driven their original demographic of loyal customers to sony and microsoft because they can provide newer technology and more innovation and creativity than nintendo can by rehashing the same characters and dried up stories over and over again. I've really grown to dislike nintendo over the years. do i flat out hate them? no, not at all. but i'm certainly not touching the wii-U with a 40 foot pole, and i haven't paid for a wii game in years (with my wii being homebrewed and all, but even then i still don't play any newer ones).
A Theory:
Nintendo has completely failed to keep up with the changing market and demographics of their consumer base. Nintendo made it big in the 80's and 90's off of young kids. we all grew up with mario and link and samus in some way or another. my older brothers grew up with the NES, and by the time i was a kid i gamed using the N64. so for the last 2 and a half decades Nintendo's main consumer base has been children usually aged 8-16. the gamecube was no match in the market for the PS2, but it was a nice step for Nintendo. good graphics, game lineup, decent third party support, and a controller that i still consider one of the best designs by far. however by the time we get to the wii Nintendo completely changed up their stradegy by cutting out hardware for gimmicky motion control, and changing their target audience to more of that 8-16 age again. The Gamecube in it's design and it's game library seemed like a good followup to the consoles of previous generations; it seemed to market itself more to the teenage customers that played the earlier consoles as children. whereas the wii has taken a step back to try and pick and choose the audiences it wants; a fresh batch of young blood, and the old loyal customer base. and this is where they have shot themselves in the foot, because anyone who was partial to nintendo at a young age will have an evolved taste in games, as well as the hardware and software builds of the consoles they play it on. and the new generation won't be familiar with all these decades-old characters they are rehashing and making references to older games on previous systems. Now with the wii-u we see another bit of the same thing, terrible third party support, hardware that at best only catches up to current standards, and another controller idea based around niche appeal.
this is why people are angry at nintendo. do we still like mario, zelda, samus, fox, and all the rest of the characters we grew up with? of course. but i think people still want those games, they just dont want to have to buy into nintendo's gimmicky bullshit these days to have to play them. i think people want nintendo to fail so they can become like Sega, a former console maker turned software-only company, which we can see and play on all systems. if nintendo goes under in the console game, than we can see super mario and metroid on sony and microsoft systems, and then we can all play our favourite nostalgic characters without having to spend hundreds of extra dollars for pointless gimmicks. i think the wii-u is nintendo's last gasp at the console market personally.