I don't think if a game has a budget of 4 million dollars, it should be more expensive than the price of a game that was developed for 3 million dollars.
But I don't think they can, in good faith, release a game like Kid Icarus, that would have a huge development team, voice actors, 3D graphic artists, years of development, etc etc and then release a sprite based game with SNES graphics, even if it has the same ammount of content, and release it for the same price. That's why, for those types of games, a downloadable 15-20 dollar price tage is much more reasonable.
It's not even so much my opinion, as a precedent that's been set. When we moved from PS2 to PS3 games, the price went up 10 dollars, and they told us that was because, typically, development from 6th to the 7th generation games cost more. Same thing happened with the DS to the 3DS, and the PSP to the Vita. Was the development cost really the 10 dollar difference between PS2 to PS3? Who knows, but I am inclined to believe them that the development cost would be at least, a little bit more.
At the end of the day, if Nintendo feels they can release a game with SNES graphics in 2012/13 for 40 dollars and still make profit off it, then hey, good for them. They're a business and that's absolutely what they'll do, and what they're allowed to do.
But on the other hand, when Capcom released the new Mega Man games, they were downloadable, via the PSN, for the fraction of the price of a retail game.