You can thank pioneering systems like Nintendo 64 and playstation for embedding these control schemes into game developers minds. When people develop games, I think the idea is to get them playing and into it as soon as possible. Even though it is fun to learn how to control what you're doing on screen, it can really break the flow of the game if its too difficult.
A good example of this would be EA's Skate series...or even a simulation racer like Forza 3.
Games these days seamlessly adapt to each others play styles, providing different control schemes if a certain game has had you playing a certain way. A good example of this in first person shooters is the melee button. Some people push the right stick in while others prefer to use the B button (360).
Meleeing in FPS shooters was classically set to B, but the advantages of not lifting your thumb off the right stick have made it ideal for the right stick.
I personally stick to my old values and use B.