Nintendo is still a little new to the whole system unification thing. From what they've been saying, they're getting better at it. But other than that, they've actually had a great track record with their e-Shop games. All of the Wii's Virtual Console games are still playable on the Wii U via the Wii Channel and the Wii's e-Shop is still accessible from there. Also, you can upgrade your old VC games on the Wii to the Wii U. You'll have to pay anywhere from 30 cents to a dollar depending on the game but it gives you Gamepad support and a proper screen ratio in return. On the 3DS, all downloadable DSi games are playable on there and the DSi shop is still accessible.
So given how Nintendo has been making slow efforts to improve their online presence and given how much care they've shown towards transferring games to newer consoles, I say go ahead and start purchasing them.