They actually have.

The scale of how much money goes back to the console maker is a sliding scale. Last generation, several high profile games came out on Gamecube for $40 instead of $50. Nintendo lowered their own royalties so that publishers would be more willing to take a smaller hit by offering the game cheaper, but likely be able to sell more units. If you have a $20 title, it pays less royalties because it's sold for cheaper than a $50 title.

Of course, there's also Virtual Console to deal with...