To clarify, if the game is a premium value product, it will be $60 regardless of platform. You're not going to see Metroid Prime 4 selling for $40 on the NXDS just because of the hardware it's on. You want premium games? You'll have to pay premium prices.
That being said, I wouldn't be surprised to see some "in the middle" games. Things like Smash NX, Mario Kart 9, Nintendo vs. Capcom (please) and Diddy Kong Racing Returns (please again) would probably be in the $50 range instead of a strict $40 or $60.
You also might see things like the next big 2D Mario, Donkey Kong, or Metroid being $40 on both platforms instead of artificially inflating the price to $60 simply because it's on a home console like with Wii U, so there's a balance.