WiiU/3DS could NOT have Wii VC due to the bad way Nintendo designed the Wii's store/VC/OS. This is why the WiiU required a completely different store (eShop) and why VC games for WiiU had to be recreated vs simply copying over Wii's VC library. Also why they asked for nominal fees to purchase the "enhanced" WiiU VC games. Basically, they asked us to chip in on the costs to recreate the VC library.
3DS was retooled to utilize this common eShop and VC structure as the WiiU. However, Nintendo had already started putting out 3DS VC games before the base OS redesign and at that point was forced to keep the two VC library disconnected for the most part. Additionally, the hardware differences still made it harder to use the same VC Rom for both platforms and thus cost prohibited to make the game once for both WiiU and 3DS.
The entire point to the NX "platform" is to have a single game shared on both systems. It will also build off of the WiiU and 3DS similar OS, eShop, and new basic Nintendo software platform. With that in mind I am willing to bet that with NX you will be able to move VC content directly over once you login. This is due to the forward thinking put into the WiiU OS/eShop/VC that was fully planned to be a platform base that can be reused as Nintendo pushed out new systems in a similar fashion as iOS and Android continuously build up new features without losing all functionality on old apps.
VC in particular will simply require updates to the VC subsystem that controls console virtualization but each rom should be modularized to be carried forward. As new consoles release, additional older consoles get added to the platform and you can continue to build up your VC collection, always a few gens behind current.







