The cross-buy system Sony has set up between the PS3/PS4/Vita is something Nintendo fans have long envied, especially when virtual console titles like Super Mario Bros. 3 grace both the Nintendo 3DS and the Wii U eShops, but you have to buy them separately on each device in order to play them.
In an interview with Kotaku, Miyamoto stated that the home console and handheld console teams being different presented a challenge to being able to unify purchases.
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 further pressed about unified purchases for virtual console games, the only answer Miyamoto gave was, “I’ll think about it.” Hmm. Sounds like something Nintendo isn’t considering too hard just yet, but there may be hope. You never know.