Consider the following hypothetical:
Existing WiiU SKU - not changed. $299 for the console with the Gamepad and Mario/LuigiU included. Sold at a loss.
New SKU - Donkey Kong Country TF bundle for $249 with the Wiimote/nunchuck/Pro Controller. Sold at a profit.
DKC would be the perfect candidate for this new SKU because it doesn't utilize the Gamepad AT ALL, other than off-TV play (which I like, but not everyone is interested in).
While a $50 drop will only spike sales so much, consider the bigger picture here. The new SKU would be profitable for Nintendo and the lower price would still sell more hardware. More hardware sold = more software sold, which results in more profit for Nintendo.
Now apply the new $250 SKU/bundle (Wiimote/nunchuck/Pro Controller and _____ game) to Mario Kart included in May; a Smash Bros bundle for the holiday. Hopefully even a Wii Sports 3 (U) bundle. Then, even the same SKU but with no game for $199.
The $299 Gamepad SKU is still perfectly available; Nintendo is just providing options for people and selling more hardware and software as a result.