1. They're slow.
2. There are far too many screens/taps necessary to do things.
Loading each new screen seems to take at least a few seconds, and there are way too many of them. I'd estimate you could remove like half the screens in the 3DS shop purchase flow through better UX design. Just compare how long it takes to buy something on either system to how long it takes on Android or iOS.
edit: oh yeah and downloading takes large games takes a REALLY long time. I downloaded the new Sonic game for my 3DS the other day on the guest wifi at a Google office and it took like 3 or 4 hours. It definitely wasn't the wifi that was the constraining factor, speed testing on my phone showed it at like 200 mbps.