So they're launching a system and they couldn't even launch with a unified store?
I can excuse some laziness on how they emulate the old digital games but to not even have it in the same store with the same economy is beyond stupid.
Given that DSiware on 3DS is fully integrated into the eshop, is purchased using the same wallet funds...
... I would theorize that they're not being "lazy" now, because they do integrate things when feasible. Rather, they're suffering the consequences of an inadequate digital infrastructure from years ago. The Wii Shop content, wiiware software packages, and virtual console games, may be utterly incompatible with the newer, account based eshop.
Keeping a separate OG Wii store may be the only way to continue to sell the old content for now. It's ugly, there's no doubt about it. But this may have been written on the wall years past.
Taking a random partially educated guess, could be the only way to resolve all this would have been:
1. Have native emulation for wiiware and complete VC catalog ported to Wii U by launch.
2. Wiiware and VC games then sold through Wii U eshop.
3. Devise a one-time-only license injection service. When transfering system content from Wii to Wii U, all digital content is permanently associated with a Wii U user account that becomes the owner, with the content playable by all users on the same system. Which is how native digital stuff works on Wii U, just like 360 and PS3.
Point #3 may have involved license renegotiation related to every wiiware rights older and VC title rights holder, in order for that software to become native to a new platform. Not impossible, but laborious and slow.
Given that the 3DS situation was handled smoothly and transparently for the end user in this regard, I'm willing to give them the benefit of a doubt that the Wii BC situation is non-trivial and involves significant hurdles.
Which isn't to say they won't perform further porting of VC content and such later on. That might happen. No way to tell though.