I personally prefer physical copies of things like games.
Lurked around the forums too much and saw some stuff about digital versions getting a corrupt data error? (Someone correct me if I'm wrong.)
Plus if you 3DS happens to break or something, you won't have to worry about if you can transfer data and whatnot.
Physical. This way if something happened to my 3Ds my game is still intact. I've seen people having trouble with transferring their games when something goes wrong with the 3ds it's self.
I have one of each....the physical copy is my main one and the e-shop one is like one to play around with. But i guess physical copy would be the best option.