The main reason I don't purchase retail games via the eshop is because they aren't linked to an account. If I lose, break, or have my 3DS stolen, I don't want to have to contact Nintendo in order for my games to be reinstated. If I get a new 3DS, I don't want to have to do a system transfer.
Accounts are just so much easier. There's a reason that everything else uses account base systems. Nintendo needs to get with the times.
But as @HarmoKnight suggested, a choice would be good for people who are afraid of having accounts hacked. Though if your account gets hacked (which is highly unlikely) I'm sure contacting Nintendo would solve the problem anyway.

