I'd almost suggest that console makers should allow a little bit of customization options on a per-game basis, to be saved along with a save file. If anyone remembers Mega Man Classic Collection on the GameCube, Capcom switched the position of the "Jump" and "Fire" button with each other, and while the switched positions weren't a bad control scheme, it was very awkward for absolutely any Mega Man fan with experience from just about any Mega Man generation.
So I've got to agree, whenever possible, offer a control scheme that mimics the original game's control schemes in ports and remakes. It's just too alienating for several people who already have experience with the game.