As a Wii U owner and lifetime Nintendo fan (owned everything except Virtual Boy...~shudder~) I have three primary bones to pick with the Wii U that I think are and will continue to lead to struggles for Nintendo:
1. "A day late, and a dollar short." The Wii U should have come out 5 years ago. As soon as Nintendo saw that they were starting to falter a bit with the software sales of Wii games outside of their own offerings, they should have forged ahead and put the rumored "Wii HD" on the market, effectively drawing even with hardware specifications with the competition. A lot of people complain, and state "well, you don't need hardware to compete - clearly the Wii outsold the competition." That's all well and good, but developers want to work with cutting edge hardware. Developers also want to be able to reach as many consumers as possible with multiplatform offerings, particularly big-sellers like the Madden franchise among others. The best way to ensure that you don't get left out in the cold is to have the hardware that developers can use.
2. Marketing Failure. "Wii U" as a name is probably about the worst name that Nintendo could have decided on. I thought that the right idea would've been calling it the Wii 2...or even just the Nintendo U (building on the Wii "we" naming convention, now shifting more to single player experience focusing on U "you"). Fanboys will of course say that it's not that bad, it's easy to distinguish, but it really isn't. I said it in another less-detailed post that gamers these days are not die hards like the rest of us - they don't read GAF, gaming websites, etc. They only know about new games coming out when they see them on TV, hear someone talk about them, or see them at GameStop. To them, there is likely no tangible difference between Wii and Wii U. This is one thing that I think has hurt them at the onset.
3. Marketing Fail, Part 2 -- multiple models/SKUs. I think just about everyone is starting to finally realize that unlike cars, we don't really care for a ton of options on our consoles, at least in my opinion. Offer one model for one price point with all the great things that you need to have a great gaming experience. Again, casual gamers don't know the difference between 8GB vs 32GB of storage space. Just split the difference for us and go with one 16GB model, or just nix the 8GB model altogether -- give us everything we need. For those of us that need more than 32GB (die hards/hardcores) we'll take advantage of the additional hard drive features, etc.
These are things, in my opinion, that have hurt the console, with #1 being the biggest going forward. In my opinion, Sony would be extremely wise to not only unveil the PlayStation 4 on February 20th, but to set the price point as well. If it's close to the Wii U's price...it's going to be tough for Nintendo to forge ahead with the somewhat anemic release schedule for 2013.
I love the console, though. For those of us that simply buy Nintendo consoles for first party titles, it's just the usual waiting game, and with Wind Waker HD approaching this fall I think it will be so, so worth the wait!