Where to start? Nintendo hardly had any major hiccups back in the day but the most notable was is sticking with cartridges for the Nintendo 64 which had to turn off publishers. It definitely impacted their relationship with then Squaresoft and how it helped Sony spiral their console in a household name. The two biggest mistakes that Nintendo has made continuously is sticking with undesired formats by sticking with cartridges and not moving to dvds. The other is not being aggressive with a competitive online gaming network.
Now though in these days or I should say the past days Nintendo didn't get when it came to what gamers want. They where out of touch with what gamers want. They should have published Xenoblade, Pandora's Tower, and The Last Story. It is ridiculous that they passed Pandora's Tower and The Last Story and waited so long to publish Xenoblade. The was basically it with the Wii. They did everything else necessary.
Launch line-ups with the 3DS and the Wii-U have been pretty bad. It was a mistake for Nintendo not have something high caliber for the 3DS. Nintendo made to do something to stir up sales since the handheld was in a slump. They made a unexpected price drop which in turn pissed off a lot of early adopters. The Wii U right now is in need of games. Pikman just came out and was suppose to be out months ago.
The biggest mistake Nintendo could be argued simply naming the Wii U, the Wii U. So many people think the Wii U is just an unneeded extension of the Wii. It didn't help that during the unveil that they didn't showcase the console itself. It would had been better fit to, if anything, name it the Wii 2. The Wii U doesn't just have an identity crisis. Nintendo has been hard on securing third parties and making their systems underpowered versus the competition can be a mistake but in hindsight, it probably wouldn't do much considering those third party are catering to those interested in more mature titles expected on its competition. Nintendo is though to blame for playing it too safe. They need new AAA IPs.
Yeah, I think even the Wii is outselling the Wii U. That's pretty bad. I never thought that the Wii U name had so much to do with their bad luck, but you are probably right. The only big game that actually made good use of the Wii U controller was Rayman Legends. And we all know the story behind that one.
I find Nintendo difficult to defend even as a fanboy. Although a lot of my gaming has been on DS/3DS/PSP/VITA, especially DS, I have no real reason to pick up the WiiU at all. You would think that Nintendo would at least put out some more virtual console games or maybe gamecube games, but no. It's like they don't care. As the new console dates approach I'm growing tired of this gen games and graphics and I'm ready for the next thing. Wind Waker is just not enough. Pokemon on the other hand, oh but wait, it's on 3DS. 
Yeah, they've had hiccups that put them behind the competition, but it's getting to where Wii U sounds like a Virtual Boy kind of mistake.
If it wasn't for Bayonetta 2, I would completely ignore the Wii U. It has games coming out for it that I would play but nothing that makes me rush out for the system. I'll just buy up games and wait for the Wii U to drop under $200 or maybe someone will buy it for me like what they did with the Wii.
I just bought a 3Dxl a couple days ago. It was on sale and with the money I got from my birthday last week, less than $100 actually came from my own hard working pockets. 
yeah naming the new console "Wii U" was definitely a mistake. Sounds like an add-on or something.
At the very least they couple have called it the super wii, or wii 64 and people would have understood. Wii 2 would have also been acceptable.
