3DS has been doing really well. (And kind of damn amazingly well if you consider how treacherous its path has been with the market fighting off cellphones, and its botched launch.) It's a damn survivor of a product, and kinda crazy to not count it as an impressive win for Nintendo.
If Iwata has been responsible for Wii, DS, and 3DS's success (despite its unfavorable beginnings), then I think it's really daft to unseat him cause of the WiiU. No doubt the man's made mistakes, but I think he's ultimately done way more good than bad.
I also really like how he's attempted to connect directly with fans more with having things like Nintendo Direct and Iwata Asks.
One flop shouldn't undo numerous other successes.