What I think would be the way to go for Nintendo is to allow the installation of apps, similar to what the 360 allows now, along with phones and tablets. The problem with the 360 is that Microsoft is the gatekeeper of all things sold and a separate games app would run against their control.
Now, Nintendo wants to be flexible with the publishers, so they could allow EA to have an Origin app, and Valve can have their Steam app, and Activision can have an app... Nintendo still tracks the sales, and if you want to monitor your account, you just visit each app. Nintendo doesn't have to maintain a history of your downloads, they don't have to monitor your credit card info, its all on each platform holder. Even online aspects can be up to the platform. I'm sure the storefronts will be specialized to the WiiU, and you can choose whether or not a particular platform is open on your system.
A weak point is a lack of an overall wallet. On the 360 and PS3, you have a unified account that has funds, and you pay MS or Sony and they redistribute the cash. Though on a PC you do have to maintain separate accounts, so its not an entirely new idea. Just throw a magnet stripe reader on the controller... lol.