Nintendo needs to support and grow their online network. They can't do that if they release their major eShop exclusives as retail games. Nintendo is only harming themselves by telling customers, like yourself, that they don't have to care about the eShop. At most they should distribute giftcards to retailers.
It's not about one or the other... They can do both. For example, they can release these games digitally first, then some time later a physical compilation for those who want it. Or, release a limited physical release through a variety of ways (promotions, preorders, specific stores, etc).
There's always people who prefer to pay less and get a digital version, and people who prefer to get a physical one even if it means paying more. Catering to all kinds of users by giving them a choice is more important than trying to "force" people into the eShop. After all, the whole point of the eShop being there is to add convenience and alternatives to buy the products, which is what matters at the end. It's a means to an end, not an end in itself. And as flagstaad mentioned before, a physical release can create awareness for your product outside the range of digital distribution.
PS: Giftcards and other kind of digital codes don't count... >.<