I guess because the design started with the genesis 6 button pad. They needed to figure out how to get six buttons on the face to make SF2 playable and maybe didn't want to make the controller much bigger.
The funny thing is the 6 face button "fight pad" layout isn't great for fighting games and most pad fighting game players prefer a PS modern style pad with 4 quality shoulder buttons. It's easier to have access to multiple buttons with different fingers than to have to move your thumb around or play claw style.
Even for shmups I'd rather have a good shoulder button on pad because I'll put extra actions (ie option switching in garegga, lock shot in ray force, C button auto etc) on the shoulder so I can leave my thumb on shot.
