Iwata is a genius when he has a clear vision and this is something he has demonstrated multiple times since becoming CEO.
The more interesting thing to observe is how Iwata deals with correcting mistakes or reacting to unexpected changes in the market. Here I believe his track record is more hit or miss:
Nintendo's first big project under his leadership was the GBA SP - I think we can all agree it was clearly a great move for the platform, and despite some oddities like removing the headphone jack, fixed almost everything that was wrong about the original GBA.
The Gamecube had already launched when he came into position, and while we don't have a complete picture of all the decisions he made during its lifetime, it's clear he wasn't able to save it. To be honest, I'm not even sure he presumed to have a plan to reverse its misfortunes. Some of his executive decisions during this time were: selling Rare, buying Monolith and other acquisitions which in the short term probably didn't have as much of an effect on the company as they did in the following generation.
NDS - while obviously remembered as the high point of his career so far, it didn't start out perfect either. The original design (aka DS phat) was clearly not ready for prime time, but Iwata corrected this misstep by releasing the Lite, which similar to the SP, I believe did wonders for the popularity of the hardware. In the DS's case it was probably what caused the turning point from a decent product to the beast it ended up being.
Wii - Started out amazingly well, with a clear message and huge appeal. The design was an immediate winner unlike the DS, and there was a pretty strong software lineup during its beginning. Demand far exceeded supply, and Iwata did his best in managing the production pipeline and anticipating the platform's continued popularity. Securing exclusivity for key Japanese franchises was also a major win in Nintendo's home territory but the western market proved to be an area where the company was less willing to take risks - possibly due to unfavorable exchange rates(?), but that is just a guess.
On the software side, there also seemed to be a loss of a clear direction after the first half of the generation.
Perhaps this was a result of external pressure due to the global economic crisis, but the previous vigor and clarity that seemingly defined Nintendo under his leadership were missing, or at least severely undermined.
3DS launched at a price that was way too high and without enough essential software, but contrary to popular belief it was still an improvement on the launch of the original DS in many aspects. People don't remember how depressing the DS was during its first year, with such releases as 'Yoshi's Touch & Go', Namco's 'Pac-Pix' and other small experimental titles like "Electroplankton", all severely lacking in content. Still the price was clearly a mistake and the market had changed considerably since the rise of app stores for smartphones. Consumers were much less patient than they were in 2004-5 so the lack of immediate essential software was more obvious. Iwata took drastic steps to cut the price for both hardware and software, which definitely helped the platform gain momentum. Once again, it's not clear if the high price and slower adoption in the west were a result of Nintendo being incapable or rather unwilling to take bigger risks outside their homeland, as the exchange rate was still highly unfavorable for them.
Wii U so far continues to suffer from the same problems as 3DS, launching at a price that is too high for immediate mass market appeal, and lacking essential software. Expectations for a platform launch have changed considerably and Nintendo has not been able to keep up. However the Wii U's future isn't certain yet, especially since for the first time in years the Yen's exchange rate is finally returning to more favorable values.
What seems to be certain however is that as time goes by, launching a new platform and bringing it the point where it is mature enough to be valuable to a wide range of consumers has become more difficult for Nintendo - i.e. it takes more time than it used to. This is actually true as far back as the original DS, and is probably a consequence of Nintendo emphasizing new, previously unproven forms of gameplay and presentation, rather than pushing for more of the same.
