You basically have 3 options:

1) re-decal the cabinet. This is time consuming - but it's the only option that will result in completely fixing the issue
2) using a hair dryer, soften the decals where it's wrinkled and push it back down with your finger. This will make it look better in most cases, but usually doesn't completely resolve the issue (and sometimes doesn't work at all).
3) re-purchase the larger leg protectors and cover the wrinkles - this may or may not cause new wrinkling around the protector depending on how tight you put the legs on/nudge the game. I've also seen the felt buff the clear off of the decal leaving a matte look where the felt touched the cabinet. I'm not a fan at all of the leg protectors and remove them from any game I buy that has them...but it would cover up the wrinkles in your situation. Here is the link: http://www.marcospecialties.com/pinball-parts/PINCAB

Damon

Just play the pinball,who cares dude?

Jack up the cab and take the leg off.

Put on a Stern style decal protector against the cab, and trace it's outline through the decal with a sharp razor knife:

http://www.pinballlife.com/index.php?p=product&id=2711

Gently warm the decal with a hair dryer.

Using the tip of the razor, gently lift the edge of the decal along where you made the cut. Re-warm the area if necessary.

Keeping the decal warm, peel back the decal. Don't stretch it. Let it stick to an old credit card so it does not re-adhere to the cab while you work your way up.

Keeping the decal warm, now smooth it back into place - free of any bubbles.

Install the Stern decal protector.

Install the leg.

Move to the next leg......

This would drive me crazy and I would need to do exactly what he is doing...finding a solution