GameCube support would require them to put more thought into control setups and probably take a bit more behind the scenes work, but it probably wouldn't be that much more work. The bigger difference there is probably that they think there's more money to be had selling Galaxy 2 than there is in Sunshine.
As for the N64, from what it sounds like it was a huge pain in the ass to get things working on the Wii, and required on ton of tweaking on a per-game basis, which is why we got so few games for it. It'd be easier to do it on Wii U than on Wii, but it'd still take work to get it up to the standards Nintendo holds itself to for the VC.