I'm curious what all the Iwata-should-step-down and Reggie-should-be-fired people think their replacements should do rectify Nintendo's woes. I haven't heard any good ones. People suggest "Get better third party support" except that's an instruction, not a strategy. Nintendo has made several plays to turn that ship around when it comes to third parties. Gamecube from a hardware standpoint was the anti-N64, a disc based, easy-to-develop-for console. Wii was the anti-Playstation, a console with an entirely different philosophy. If third parties didn't want to support a console that went head to head with Sony (because they can just support Sony and be content), maybe they'll support a console very different from it.
See, Nintendo has tried; their strategies just haven't worked. They weren't bad ideas, but Nintendo, unfortunately got stonewalled anyway. I don't think that's necessarily Iwata's fault. Would someone else have been able to do better? Maybe, maybe not. I'm leaning toward "not" because if you look back, Nintendo's problems go all the way back to the NES and SNES. They got support begrudgingly. Nintendo was building bad will generation after generation and it's hard to come back from that.
Since Nintendo doesn't have a time machine to prevent those rifts with third parties before they happen, it seems like their main issue right now is the lack of their own software because it's rather difficult to make money without things to sell. That is partially Iwata's fault, but I'd rather Nintendo continue withholding games until they're finished than trotting out poorly made garbage just to have something out. That's a possible reality with someone else in charge. That's even shorter sighted thinking than we're used to from Nintendo. Replacing Iwata doesn't sound like such a fantastic idea in that case, does it?
When Iwata succeeded Yamauchi, it was planned and they had a strategy in place which, again, didn't work, but at least the transition was smooth. If someone replaced Iwata, they're "stuck" with the Wii U for the next few years. It's quite a bit more complicated for a hardware company like Nintendo. "Hi, I'm new. Make games for us, plz?"
Ultimately, I think Nintendo will be okay after this rocky start once their games start coming out. Listening to third parties' faulty reasoning for not supporting Wii U, they weren't going to support Wii U with or without better hardware, so I'm content with what Nintendo released because $350 was pushing it, any more would have been an immediate no sale.
Still, that only takes care of one of Nintendo's issues and the others need to be addressed. Restructuring their hardware divisions was an important and underrated move as well as a good start. It's a shame how far apart Nintendo's consoles and handhelds are and have been. I'm surprised this took so long. There have been minor efforts to get them to work together, but really, they barely connect and that was wasteful.
As far as third parties go, Nintendo should spend the next 2-3 years interviewing and reinterviewing every publisher, developer, and middleware provider separately (which is important because they'll all give different answers) and ask what they want from the next handheld and console for say, a 2016 launch for both. That cuts the Wii U lifespan a bit shorter than their other consoles, but that may be for the best and it's not without precedent. Microsoft replaced Xbox in four years and Nintendo themselves effectively replaced GBA in three and a half. Nintendo won't fill every request, but they should get the basics right as many will ask for the same things. This is something Iwata can do, but if someone else is tasked with it, they really should start now.