Thanks to Spudz for finding the first batch of Character Icon Flip Buttons. Look at Sub-Zeros and see what buttons it maches up to. What you do is goto your character you wish to flip and hold Start and hit the 3 buttons and then while it shows the yin yang pick your character to get their alternate color.
Scorpion: Hold Start, HP+HK+BL
Johnny Cage: Hold Start, RN+LP+LK
Sub-Zero: Hold Start, RN+BL+HP
Reptile: Hold Start, LP+BL+LK