The one thing that strikes me whenever Nintendo software drought is discussed regarding the last generation, is that Nintendo didn't have any problem, overall, with the DS side of things. They pumped software out for that thing like there was no tomorrow. But that may be the key. The smaller scale of DS software development may have allowed them to do so with the resources they had during those years.
While there have been rumors of sorts about Nintendo expanding, one concrete statement from Nintendo was found in the Iwata Asks for NSMB2 - they made it sound like that game was all but purposefully a training project for young developers being brought on and educated to enter the big leagues. And where it counted, level design, NSMB2 was a good proof of concept for that. It was high quality in terms of what the new guys were being trained for (level creation, course design).
So perhaps Nintendo is, in reality, dramatically expanding their development capacity. Developing large scale console games is difficult while maintaining Nintendo's desired level of quality control and final product polish. Even with the Wii, games like Mario Galaxy and Skyward Sword don't just fall off a truck. Regardless of the size of the teams involved in each game, it's also about talent - which experienced staff are available to work on critical aspects of each project. In point of fact, just because we might look on from the outside and believe that Nintendo has enough total staff to make a 3D Mario, Starfox, F-Zero, Metroid, Zelda, and "New AAA IP" at the same time, they might not have a fraction of key talent to make all that within a staggered 2 year dev cycle for various games.