I don't doubt that unforeseen problems attend managers all the time, but he owns those as much as if he had gotten a lucky break.
Nor do I doubt his sincerity or his desire that things were better. I think it's inspiring he took responsibility for the 3DS failing to meet projects and got a paycut. I also think he genuinely cares about gaming in a way the beancounters at Microsoft do not.
But that doesn't absolve him of misdiagnosing problems or for failing to consider the very obvious issues of reputation his company now faces. If he was new to this, there might be more benefit of the doubt, but when problems are repeated, continue, or grow in ways that are frustrating to observe as a customer, it's hard to extend that benefit.
The fact that this system came out with a well-designed but ultimately uninspiring 2D Mario game is not a "solution" to the 3DS' problem; it's a misreading of what went wrong with the 3DS: its price and lack of compelling software, coupled with almost no support, first-party or otherwise.
The fact that Nintendo struggles to develop HD games when they had plenty of time, resources (from the Wii years), and evidence (from other developers), is disconcerting too. First party support for the Wii basically dried up in the last 2-3 years, which suggested they were working on something, but 2 E3s went by with nothing to show for it. You're right that it's silly to "write the Wii U off when [x, y, z] haven't released," but where are x, y, and z? Problems with development should have been anticipated, but weren't, for some reason.
And, purely from a business standpoint, he's bet on the wrong horse twice with the 3D on the 3DS and the touchscreen controller on the Wii U. That's pretty catastrophic that he was unable to sell these innovations/gimmicks, because he based huge parts of their production costs on features that the mass market finds no value in, and left him with little room to maneuver in some cases. You can't say that's a brilliant business move.
And this is to say nothing about Nintendo's continued insistence on backwards online account systems, although it seems they are moving (however agonizingly slowly) to better online implementation.
I like Iwata, but he's engendered some dangerous practices, some within his control and others that were easily foreseeable and correctable had he the gumption to step on the brakes.