This was something I posted before E3 2011. Many of the concepts now seem unlikely given that the Wii U might not even be able to support multiple gamepads, but I still think the ideas themselves had some potential.
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Super Mario -  Some of the best moments in Super Mario Galaxy 2 were those sections  where you dropped down one of those infamous mushroom kingdom pipes and  found yourself on the other end playing a classic 2-D Mario level. What  made these sections so cool was that one minute you could be flying in  3D space around a spherical planet and the next you would be jumping and  hopping on a 2D plain as if the last 20 years of video game  developement had never happened. It was great. So why not build upon and  emphasise this concept by having those 2D portions put on the Cafe  controller screen? You could even have simultaneous play on both screens  ala Bower's Inside Story. It's true that this style of game play was  seen on the DS and is likely to be seen on the 3DS, but if Project Cafe  is (as is reported) more powerful than any of the home consoles  currently on the market then the scope afforded to this sort of game  would be significantly expanded.  
Television Screen   Controller Screen
  Controller Screen   Metroid
 Metroid - Metroid: Other M may not be the most loved in the series, but it  definitely had some cool and interesting ideas. One such idea was the  concept of shifting between the third and first person perspective.  Unfortunately this concept was hindered somewhat by Director Yoshiro  Sakamoto's decision to cram all of the required gameplay mechanics onto a  single Wii Remote (even refusing to utilise the nunchuck to provide an  optional alternative control scheme for those who desired it). This  choice had some pretty serious repurcussions for how the game played, as  it effectively meant that the player was forced to continually change  their grip on the Wii remote in order to point it at the screen. Enter  Project Cafe. Third Person action game on the main screen, first person  shooting with the touch screen on the controller. Problem solved. 
Knowing what I now know about the controller's built-in gyroscopes I would also add that holding the controller up to the television screen might provide quite an elegant solution for scanning environments. As good as the method for selecting visors was in Metroid Prime 3, this could be even better.  
Television Screen   Controller Screen
  Controller Screen   Pikmin
  Pikmin - Pikmin 2 was a fantastic game. It took the original lite strategy  elements of the original and expanded upon them in pretty much every  way. The final level of the original, for instance, required our plucky  protagonist Captain Olimar to move back and forth between several groups  of Pikmin, each of which were performing different tasks which had to  be timed in order to allow the other groups of pikmin to continue.  Pikmin 2 took this idea and ran with it thanks to the inclusion of  Captain Olimar's sidekick Louie. In Pikmin 2, therefore, the player was  tasked with switching between both characters as each led their own band  of Pikmin to perform various goals. Fun though it was, it did on  occasion feel overwhelming as it was often difficult to find your  bearings as the camera switched between the two locations. Having both  groups of Pikmin viewable at any one time, one group on the television  and another on the controller, would do much to mitigate this confusion.  
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Bonus Idea - You can grow and tend to your Pikmin crop/farm on the controller  screen without the need to go back to base. Damn it I'm good.***  
Television Screen   Controller Screen
  Controller Screen   Street Fighter
   Street Fighter  - We've all experienced it. You sit down with a buddy to play a  friendly bout of Street Fighter. With each match, however, the  testosterone in the atmosphere builds and both partys begin to take the  virtual fight increasingly more serious. Eventually half your time is  spent waiting for your 'buddy' who has paused the game in order to  review their move list. Throw that stuff to the controller screen.  Problem solved.  
Television Screen   Controller Screen
  Controller Screen   Paper Mario/Yoshi's Island
   Paper Mario/Yoshi's Island - Nintendo have a history of creating art styles which are patterned  (pun intended) after real world arts & crafts, with games like Paper  Mario, Yoshi's Island, WarioWare and most recently Kirby's Epic Yarn.  When Ubisoft released the uDraw peripheral back in November I remember  thinking how cool it would be if Nintendo were to use something similar  to allow gamers to contribute their own art to a game. Think Mario Paint  meets Okami meets Drawn to Life. I love the idea, for instance, of  drawing some wacky little character only for them to return as an enemy  later in the game. You've all seen that Spongebob episode right? Well,  it would be like that but with Bowser instead of Squidward and Yoshi  instead of Garry.  
Television Screen   Controller Screen
  Controller Screen   Super Smash Bros.
   Super Smash Bros. - Last but not least, Nintendo's flagship multiplayer mashup, Super  Smash Bros. The best thing about Smash Bros. of course is getting three  friends around the television (either with items on or off, depending on  your preference) and beating the hell out of each other. There is,  however, one thing about the current set-up which can kill some of the  enjoyment, and that's being put out of the brawl at an early stage and  being resigned to a mere spectator. That's where the controller screen  comes in. Rather than making the losers sit there watching the more  experienced players battle it out for the top spot, why not allow them  to drop  down to the controller screen to duke it out for third place?  That way everyone's having fun.  
Television Screen   Controller Screen
  Controller Screen  