It should also be noted that your Cut the Rope example in the main post, is a DSiWare game; not an eShop game.
DSiWare on the 3DS (like Plants vs Zombies) look worse when stretched on the 3DS; but quite sharp scaled down on the 3DS or at the native-res on the DSlite/i/XL screen.
Not "as sharp" as iDevices/Androids/etc. but not horrible or even bad. Heck, many still prefer playing the DS/DSiWare games on the respective handhelds because of that.
Me? Hardware costs is usually low for me compared to the total software costs for a whole generation, paying $100 or $150 for a Wii U hires controller that can compete with iPad games when it comes to smaller eshop games would be no problem at all for me.
Keep in mind that the controller is not just a screen. Even Sony is losing money with the $250 Vita; so is not like the Wii U controller with everything it has and a higher-res screen will make it on the $100/$150. Even more when accessories are also marked up in prices for the sake of profits.
And so far, from what it is known all games have to be done at whatever resolution they want it on Wii U (up to 1080p); and that's what will be scaled down on the 640x480; which will still make for a nice image.
It is also known that when making games that use heavily the controller, it takes resources from the hardware.