With the exception of TMNT, I imagine they'll all transfer over to Wii U. I doubt Nintendo will make an account-based system though, as there isn't one for the eShop.
Nintendo just needs to push their online shop more, and that's how they'll get more digital goods. In addition, they need an account system. It's the main reason why sales on WSC stopped because people ran into the issue of their systems dying and they couldn't transfer them over to a new system.
That and they saw the sales on SMB All Stars and wondered "hey, I think we're onto something here, cha-ching".