If there's one thing that's always somewhat irked me about Nintendo, it's the way that they approach online interactions. It never seems to be convenient. But Nintendo is aware of the problem and will be taking steps to offer new ways for customers to access the 3DS eShop and purchase content via PCs and smartphones. Announced during today's presentation to investors, the feature is still being developed and won't be included in the upcoming 3DS update.
Don't worry. Poppa Nintendo has your back. See, with the update coming in November, you will be able to scan QR codes to open pages within the eShop. That means you could look up the game on your PC or smartphone and find its QR code, then conveniently scan it with your 3DS and make the purchase. I wish I were joking when I said that this method was actually described as a part of the presentation.
Seriously. I couldn't make this up if I tried:
Baby steps, I guess.
Semi-Annual Financial Results Briefing [Nintendo]
Nintendo's big release schedule for Never Alone, Don't Starve, and lots of other indies
12:45 PM on 03.04.2015