For the most part, Nintendo's development teams that focus on handheld games are different than the development teams that focus on console games; and the decline in released software for one platform is typically unrelated to what is happening on other platforms.
Personally, I suspect that the decline in Wii games would be (in part) related to Nintendo devoting resources towards their next generation home console. With a team that was experienced with HD development and was fully staffed to support projects on that scale one would expect 3 years of development for premiere games, and 18 to 24 months for more rushed projects. Nintendo’s teams are not experienced or fully staffed to complete those kinds of projects, so it would likely be more time consuming and require Nintendo to expand many teams rapidly.
Even if Nintendo takes full advantage of outsourcing, and expands the size of the company through acquiring competent developers, many of their development teams would be focused on next generation development today regardless of whether the system was being released in 2012 or 2013.
If my hypothesis is correct, I would expect to see Nintendo announce more partnerships with third party developers/publishers to produce well known Nintendo series (F-Zero, Starfox, etc.) for the Wii; and the number of Nintendo developed Wii games to remain fairly limited.