Kid Icarus: Uprising is that, even though it induces carpal-tunnel syndrome, it's just so gosh-darned fun. Developer Project Sora's director Masahiro Sakurai has offered some insight into the control scheme and some tips for a more comfortable gaming experience – beyond "use the stand," that is.
"I think any game needs to provide new experiences and stimulating things to discover, but if we provided run-of-the-mill controls for it, that cuts down on the game's potential," Sakurai told IGN. "If a player used to touchscreen-based aiming played against someone used to right-analog control, the first player would probably dominate. The speed is on a whole different level."
As for the pain in your hand, Sakurai has an easy solution: relax. "If there are players who say that it makes their hand tired, that's because you're applying too much force. Try to relax and work on building a rhythm to your control. Place the pen in the middle of the touchscreen; when you're flicking it, take the pen off the screen as you're sweeping with it, and stop right there. That's the basic idea." So in short, don't press too hard and try to be more elegant in your wrist control – it takes practice.
Oh, and if you're a lefty, just know how lucky you are to be able to play Kid Icarus: Uprising with a Circle Pad Pro – left-handed controls almost didn't make their way into the game. "Considering how close to the limit we pushed the 3DS during development, it's a miracle that we were even able to provide support for left-handed controls at the point of completion. Providing support for independent analog control was something that was technically impossible."