I was playing some Street Fighter EX a while back and what I really liked about it was the fact that Sakura was able to charge up her Hadouken by rapidly pressing the punch button. What if something like that was introduced to MK? Persoanlly I think it would be kind of nice to have control on how effective a special attack is and how much damage it does. It obviously be used for projectile attacks only. There could be a small power meter under each character's life bar to indicate three evels of attack. The attack would be done like the normal input, but the final button press would need to be pressed repeatedly to charge up power for the variations.
This could add a bit more variety and give button mashing a purpose.

For example:
Sub-Zero's Ice Blast could be the standard freeze on level 1.
On level 2 it could be a version of his Deep Freeze where it lasts much longer and the opponent could take some damage because it's much colder.
Level 3 would be his strongest and he would be able to shoot out a blast which splits into three seperate versions of the 2nd blast covering a much larger area.

Scorpion: For him it could work for his spear.
Level 1 could be the standard spear
Level 2 can have it shooting out of the ground, tangling the opponent and slamming them into the ground on a retract
Level 3 could have it on fire, and constrict the opponent for several seconds while buring them.