Quoted By:
Digital
+Very convenient, always with you
+Download at midnight on launch
-If something bad happens to your 3DS, you are fucked
-Can't resell it later
Physical
+Tangible product, as long as the cartridge isn't stolen/smashed with a hammer your save is safe
+Potentially some goodies (steelbook case/small figure) depending on where you live
+Might be able to get it before launch if you search around
-Really annoying to switch cartridges if you want to play different games while on the go, need to carry around some kind of case for storage if you aren't some kind of mongoloid who carries around loose cartridges in your pocket
tl;dr:
Paranoid/like having something to look at on your shelf? Physical.
Out of the house often? Digital.