1. I buy entertainment product
2. Using entertainment product causes me physical pain, though it is not intended to do so.
3. It must be me who's fucked up, not the entertainment product.
Makes sense!
For the record I like the Kid Icarus overall and am on about mission 15 I believe. I play for about half hour every night before I go to bed. The game is clever and I love the witty writing. But ugh, my right hand hurts so fucking bad after just a little playtime. Saying that I should just "suck it up" and stop complaining is absolutely ridiculous. The second that Sakurai realized that sitting at a table and using and extra stand is the most comfortable way to play the game, red flags should have been shooting in the air. The control scheme is unnatural and it hurts my hand. That's really all there is to it.
If you read the article, Sakurai's advice for people whose hands are cramping is that they might be pressing too hard. Not trying to be a dick, but is it possible that's the case? He also advises lighter, flicking movements.
I honestly think his statements weren't intended as, "Suck it up and deal with it, babies," but rather that the game was designed in a certain style and to be played a particular way, so knowing these things might make it more approachable for those who are finding it uncomfortable. Maybe you're already trying those things and it doesn't work for you, but just a suggestion. I know the instinct when first playing the game is to press down on the screen since that's kind of the case with a lot of touch screen heavy games. (Hence why a lot of rhythm games have ruined a lot of screens.)