I've yet to see a 2D fighter that has done that, and there's a reason:
1. That's a character slot.
2. You have to adjust the hitbox to make sure your alternate costumes don't ruin anything.
With 3D fighters, it's a MUCH easier process, since you just draw a highly detailed image and then merge it with 3D model, you only have to do the animation once or twice. Drawing the skin isn't so easy, but still.. it's a straight forward process.
In 2D fighters, you have to redraw every frame. You can take shortcuts, but trust me, fighting games have a lot of frames. To make matters worse, fighting games have hit boxes, when you make an alternate costume, you have to adjust the hitbox so that the costume don't shrink or increase the hitbox size. (No one should get hit in the hat and get hurt etc.)
Also you have to make sure the character's attack range doesn't increase or decrease.
Even SF4 and MK9 have these problems and they are 3D games.
I can show you a good example of what I mean. When I was a kid, I tried making a One Piece fighting game for PC:
Did you notice that the moves where Luffy stretches didn't work fully? (The pistol didn't carry the enemy the full duration, the hand didn't grab, the spear didn't hit)
It's because I extended Luffy's stretch size for the arm. but NOT the hitbox to go with it. If I gave Luffy a point hat of 10 pixels high, I would have to move the hit box 10 pixels lower to make it match the original.
It's a hassle for 2D programmers, and just a glitchy mess waiting to happen unless you have a nice orchestrated programming team.
It's just not going to happen.
Programmers use alt colors for this very reason, it still takes up a character slot, but it doesn't mess with the hit boxes.
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