Many things are puzzling when it comes to Nintendo and online. They can be extremely progressive at times, but they're usually ass backwards. I sometimes wonder if they're just trying to be different for the hell of it, even though they know their approach is stupid.The lack of an OS-level messaging system is puzzling, considering even the Wii had one. With terrible delays, but it was there.
A great recent example is Pushmo. You can export your levels to QR codes. You can upload those QR codes to the internet directly from the built in browser, which is something I honestly didn't know or expect. You can also save images from the browser to your SD card. But you can't import a QR code directly from the browser, or your photo album. Makes no sense at all...
EDIT: Nintendo should also implement eShop and friend code URIs. Like "eshop://pushmo" to look up Pushmo on the eShop from within the browser or "wfc://1234-5678-9012/wsippel" to add someone to your friend list.