Wii U Virtual Console versions of games are incompatible with saves from the Wii Virtual Console counterparts, Nintendo informed Kotaku.
That isn’t to say your Wii Virtual Console saves are lost. They’re still be playable on Wii U, it’s just that these saves cannot be used with Wii U Virtual Console versions of the same game. In other words, if you want controller customization, save states, and independent play on the GamePad, you’re going to need to repurchase those titles ($1 for NES games, $1.50 for SNES) and start all over again.
None of the Wii U Virtual Console perks are available for Wii Virtual Console games—no GamePad play, no save states, no customized controller configurations. If you want those, you gots to pony up.