Because they're losing ground in the big console market.
The Wii-U, by all accounts, is a console marketed at a demographic that isn't as large as Nintendo hoped (They tried to repeat the Wii's success model, market the console to people who are not core gamers, and use first party titles to keep up appearances), and saddled down with a lack of third party support.
The 3DS and its derivatives are the moneymakers for them at the moment, and THAT market is getting undercut by the smartphone and tablet market out there. Releasing versions of their games on those platforms, but not committing fully to them, is them trying to have their cake and eat it. They want to tap into the Android/iOS market, but they still want to do their main development on their own homebrew platform.
Nintendo isn't finished, no. Not by a long shot. But there's going to be quite a few changes in the way they go about their business, I think.