Why would they stop production if its selling!!!

Maybe they just wanted to use Splatoon for a holiday hardware boost in Japan.

Maybe they finally went through their unsold 2012 inventory.

One of a number of classic sales move, the bundle was to establish the game more so then the platform because Nintendo do well during the holiday season regardless so they used that as well as the game's increasing popularity and the bundle to maximize the holiday run, the game is now in demand so the platform will sell to those seeking it regardless.

Nintendo really struck gold with Splatoon.

Wait a sec. I thought that the Splatoon bundle was just repackaged unsold systems. If Nintendo is producing new WiiU systems, why not make a refresh?

They don't want to give the haters more reasons to say that Splatoon only sells because it's bundled.

its quite simple, they're aware that people are buying that specific bundle FOR Splatoon, because of Splatoon, and figure that they might as well discontinue the bundle since people in Japan will mostly likely buy another Wii U Bundle and then Splatoon as solo software if they want to play it

essentially Splatoon's popularity has made it irrelevant as bundle in Japan. you bundle a game generally to push sales and sometimes take a loss on that particular software to do that

Nintendo realizes that Japan fans will buy a different bundle and buy Splatoon as well anyway

sometimes thats how things work out. if Nintendo has a load of other bundles in inventory still then obviously it would make sense that they would attempt to push those instead of making more Splatoon bundles. you don't want excess extra bundles that are less desirable laying around, especially if you're doing well with the platform (at least in Japan)

That makes a lot of sense to me.

Well that sucks.