I strongly suspect that the way Nintendo currently handles digital licenses is affected, to a degree, by their reluctance to deal with the overhead of managing account transactions related to security.
In other words, fraud, stolen accounts, etc. It's not really possible to scam people out of a Nintendo Network account on Wii U, log in as them elsewhere, and download stuff they own. Or spend money off their credit card. These are big problems faced by all the other digital platforms, and each platform has its own security strategy.
For Nintendo to get into that, seems as if it would require a significant increase in the size of their customer service divisions in each region. Right now, no matter how much a savvy enthusiast dislikes the way their digital stuff works, problems only affect a small minority. A relatively tiny number of Wii U consoles get sent in for repair and need to have digital content licenses transferred. It all happens in their existing product servicing pipeline.
Competing with everybody else's digital services directly would require Nintendo opening themselves up as a target to mass hacks, account theft, fraud, etc.
And unfortunately for Nintendo, they're going to have to bite the bullet sooner or later. They need to develop their own version of a comparable content licensing system. Who knows, the moves they're making currently may be a part of that - for example, allowing users to fully log into Nintendo's website with their NNiD for Miiverse makes sense as a groundwork for providing online tools to manage console authorizations and digital content. (As how things work on the 360, for instance.)
I don't think Nintendo want games tied to accounts, because that stops them reselling the software to you each generation and on both handhelds and consoles.
Sony and Microsoft tie all their digital purchases to accounts. That doesn't mean you'll be able to download your PSN games on PS4. It's probably going to be the same for Microsoft too.
So for all practical intents, those platforms will end up as "backwards" as Nintendo. Though as as pointed out above, Nintendo supported transfering DSiWare to 3DS and Wiiware/VC to Wii U.