As Nintendo is going to link the 3DS and Wii U at some point with Miiverse and Nintendo Network functionality, I hope they do the same with the eShop.
Basically, I want a new eShop design that will link the categories from Wii U and 3DS together, be able to view them on both consoles, share the same balance (so you can put more money on your account on your 3DS and use it on your Wii U, and vice versa), and add a cloud storage feature.
And what this cloud storage feature could be used for, aside from just storing your stuff on there, is that it could allow you to download Wii U stuff on the 3DS and vice versa, but you can only use them on their appropriate consoles. Say you're out on a trip somewhere, and you brought your 3DS. You browse the Wii U's digital selection and see a game that you'd love to be able to play when you get back. You purchase it and it gets put to your cloud storage account. When you get back, you can download it from your cloud storage on your Wii U and voila, you got yourself a nice game to play.
They could easily segregate the content by giving clear "Wii U", "3DS", and "mobile" categories, and then extensive sub-categories in each. --- Come see my game collection: http://www.backloggery.com/bakonbitz