Buried in the earlier release about the Nindies Showcase, Nintendo had an interesting announcement about the Virtual Console:
Virtual Console games will not be available on Nintendo Switch at launch. We will share more information in the future.
Nintendo has always taken their time with the Virtual Console. Instead of releasing straight ROM dumps, Nintendo works to ensure the highest level of emulation for each, individual game. Since the NES Classic ran on an ARM chipset, this bodes well for the quality of emulation of NES games already available for the Nintendo Switch.
Since the Virtual Console will not be available at launch, this means Nintendo has not announced details regarding bringing your Wii U or Nintendo 3DS VC games forward to the Switch. Remain hopeful, though, as Nintendo is already taking steps towards unifying your Nintendo account!
People who already have funds in their accounts on other Nintendo devices can access them using a shared wallet that works on Nintendo Switch as well. Once they link their Nintendo Network ID and Nintendo Account and then their Nintendo Account to their Nintendo Switch system, this functionality becomes possible.
If Nintendo can share your wallet across generations, hopefully the game library will similarly be shared across generations.