Nintendo has had the worst digital support of all three consoles for a long time. While every PS and XB user has been able to easily transfer access between consoles, Nintendo has made it a huge pain in the ass at every turn.
While their shitty treatment of Wii to Wii U VC stuff is annoying, my reluctance to buy digital stems from the fact that it's a huge pain to get your stuff onto a new console should you upgrade (say from 3DS to n3DS), sell/trade your old console and get a new one, or lose/break your system.
On say, the PS3 or PS4, I could throw my old system in the trash and buy a new one, and getting all my games is as easy as signing in to the new system. This is not the case with Nintendo, and until it is, I won't suggest anyone buy digitally if there's an equivalent retail version (which isn't often the case with VC, of course).