I was writing up a Pro/Con list on the other thread before it was locked, if you'd waited you mightn't have needed to make this thread. Here it is:

Digital Copy:

Cons:
-No Novelty of having the packaging.
-Possible to lose through data corruption or braking of 3DS to an unusable state.
-Unable to use on any other 3DS.
-Fixed Price, slightly more expensive than Recommended Retail Price.

Pros:
-Being installed into the 3DS itself, you can play it whenever without the hassle of switching cards.
-Club Nintendo bonus.
-You don't even have to leave your house to get the game.
-You can't lose your game card since you don't have one.

Physical Copy:

Cons:

-You have to keep switching Game Cards if you have many games.
-The Game Card can go missing.
-No Club Nintendo bonus.
-Shops might not have the game in stock.
-Game Card may be faulty.

Pros:

-You can use it on any 3DS you want.
-You get the packaging and Quick Guide alongside it.
-You can get it cheaper than the eShop price, even more depending on where you look.
-If you lose your 3DS, you don't lose the game as well.