Have you seen Square Enix's pricing in the app store? They charge 20-30 dollars a game. I think Nintendo could get away with a 30 dollar Mario game in the app store.
Mind you, the majority of Nintendo Fans have a 3DS already.
But this is definitely the minority of the games that Nintendo makes. The thought of playing something moderately fast-pace like "Mario Tennis" on a touch screen scares me. There isn't enough precision, and no touch screen is as responsive as a controller yet.
The major brands: Mario, Zelda, Metroid, Kid Icarus, Donkey Kong require speed and precision beyond that of the touchscreen. Let alone the issue of blocking the screen as you play the game.