Biggest pain point for the Nintendo eShop? If you own a 3DS and a Wii U and want to own a Virtual Console game for both - you're stuck with buying it two times.
Honest question, I don't know. Just wondering if Nintendo is continuing the trend or if they're still stuck in the past.
Yes. For example, they used to sell "PS Classics", Playstation games through their store. I bought Symphony of the Night once, and had it on my PSP, PS3, and PS Vita. I'm sure you could get it on the PS4 as well.
Microsoft has a similar thing for their Xbox Live Arcade games on the xbone, but many of those are being made into HD Remasters instead of being ported.
Some games are cross-buy. Others are not. PSone Classics titles are cross-buy. Final Fantasy X/X2 HD is cross-save, but not cross buy.
There are a few cross-buy games on Nintendo systems, Severed is the most recent example. Most of Nintendo's cross-buy games have been rolled out since the new Nintendo Account system that debuted with Miitomo.