The first problem is one of perception. I'm looking at you, Nintendo fans!
Not really just Nintendo fans, though. I think everyone in the gaming circle needs to realize that things have changed. The Wii was an aberration that probably won't come again anytime soon and mobile devices have hit Nintendo the hardest. I don't want to throw around labels but there are many different types of gamers out there and one of Nintendo's staple groups has always been the more simple, pick-up-and-play type--a style that is easier to manage on smart phones and tablets than the more story-driven blockbuster games that drive the Playstation and Xbox brands.
The truth is, we need to accept that Nintendo's baseline, at least for the foreseeable future, is going to be lower than the other two, barring they pull another viral experience out of their hat. There is nothing wrong with that, either. They can make a cheaper console with cheaper game development and still do very well for themselves. Their own software sells very well--they just need to turn a profit on everything. Nintendo needs to stay away from the loss leading approach.
Beyond that, they REALLY need to work on their corporate culture. It's holding the company back and hurting their audience.
First, they need to look into more western input, leadership, and title development. It can be argued that part of Playstation's recent success has to do with Mark Cerny, the fact that they supposedly garnered a great amount of input from Naughty Dog and Santa Monica, and Yoshida-san's knowledge and familiarity with the west. Gaming is no longer ruled from Japan. It's global.
Second, on a related note, several western developers have said that they had no contact with Nintendo before the Wii U launch, while Microsoft and Sony were constantly in touch. That, to me, is inexcusable. I don't care if the odds were 90% that Gearbox or Bethesda wouldn't have made a Wii U game, YOU STILL TRY. I don't know what the problem is, if it's because the western offices have little power or if they're just not trying very hard, but that needs to be fixed. Nintendo is no longer in a position where they can dictate terms.
Third, pay attention to everyone else, damn it. You can still do your own thing creatively while making sure your competitors don't pull ahead of you. This is basic business. If someone else comes up with an innovation that's superior to your solution, you jump on that train (especially if you don't even have a solution). That is how you give your customers the best experience. There is no excuse for not having an account system, for example, when everyone else has had it for years. There is no excuse to be caught flat-footed by High Def development when everyone went through this years ago. It feels like arrogance, like they don't need to give their customers the best because they'll come running anyway.
Fourth, money. Nintendo has it. As anyone in business knows, you have to invest money to make money. Nintendo has failed to do this. They've been cheapskates and it's finally bitten them in the ass. Their development umbrella should be bigger. Their research teams needs to be better. Their advertising should be more robust. There are so many areas where spending more would have helped the Wii U in its early stages. Why has Sony's broke ass left them in the dust? Because they've been spending money to make money.
All of this should have been done years ago, by the tail-end of the Wii at the very least. The hard truth is that Nintendo has a lot of work to do, starting with an unapologetic self-analysis.