He will 'think about it'
Sony has a Cross-Buy system out for its digital storefront, and it's pretty amazing. For select games if you buy them once, you'll have access on up to three systems depending on the game -- PS3, PS4, and Vita (sometimes the PSP is the fourth).
Microsoft is a bit slow in adapting this policy on the Xbox 360 and Xbox One, but it would make even more sense for Nintendo in regards to 3DS and Wii U Virtual Console games, which have almost full feature parity between the two platforms. We've been clamoring for this for a long while, but we're going to have to wait a little longer, it seems.
Speaking to Kotaku, Miyamoto stated, "What I can say is, certainly, within Nintendo the fact that our development environment for our home console is different from the development environment for our portable system is certainly an area of stress or challenge for the development teams. So as we move forward, we're going to look at what we can do to unify the two development environments."
When pressed on whether or not players will be able to pay once for the 3DS and Wii U versions of a Virtual Console game in particular, Miyamoto said, "I'll think about it." So yep -- keep on waiting/dreaming, people.