I own all the Nintendo platforms, and there's a big chance I'll invest in future hardware.
I really dislike the idea that if I buy a game on the virtual console for Wii U, that I can't play it on the 3DS (or future hardware for that matter, given that we had to pay money to "upgrade" from Wii to Wii U, or rely on the fact that Wii U is backwards compatible with Wii, thus going through the Wii virtual OS on Wii U). Especially NES, SNES and N64 games which clearly could run on both the handheld and home console hardware.
Does this turn you off purchasing VC games altogether? Personally, I skipped out on the entire Wii generation, I did not buy a single VC game because of this concern. Now fast forward to Wii/3DS gen, I've only bought Earthbound (simply because to me, that's like a brand new game). Other than that, I refuse buying these games until I am assured that I won't need to re-buy them in future.
it's ridiculous that I need to pay for SMB 3 on both the Wii U and 3DS VC instead of just one tied to my Nintendo account. Are you deterred from buying VC altogether because of this fact?
Follow up questions, do you think Nintendo will change this in the near future? Given that they've begun baby steps in this direction. I really hope they do it soon, that way I'll splash out and buy a large quantity of retro games on the VC.