But you can have more than one a Wii U.
So create an extra Nintendo Network ID for each of you 3DS/2DS consoles. If you have seperate 3DS balances you should be able to use both of them on the Wii U I would think.
No way to get your Wii U balance to multple 3DS consoles though. You can probably use the 3DS transfer feature though I guess to move your purchases around.