Games you get on the Wii Shop Channel in Wii Mode are incompatible with the Wii U GamePad or Wii U accessories (such as the Wii U Pro Controller.) They may require a Wii Remote or a Wii Classic Controller to use.
In the future, Nintendo may offer updated versions of Virtual Console games that ARE compatible with the Wii U. Any such games you could upgrade to for a price if you bought them on Wii Shop Channel. 