Probably a major hassle to try to fix the cracks - you could clean the cracks as well as possible and put mylar squares under the spots (should have these anyways) and maybe that will hide the imperfections.

I'd like to hear some more suggestions. I was told that the cracking clear and paint on my diamond plate T2 (at the ball drops) should have a thick layer of wax down before I put mylar squares down to keep the paint from peeling up if I ever remove them. This seems odd to me, wont the wax keep the mylar from sticking completely?

Depends on your skill level, ability to work with two part clear and the type of cracks. If they're fine cracks you'll want to widen them out into a v-shape so the clear can get into them. If the cracks are wider you'll just need to clean up the edges a little. After the prep just apply 2K clear to the area to fill in the cracks and indentation.

There's also a post where they're using UV curable resin to fill in cupped inserts (the concept would be the same). I'll add the link in a minute.

If the playfield has been clear-coated you don't need to worry about the wax/mylar approach since the paint is protected from lifting by the clear.

http://pinside.com/pinball/forum/topic/how-to-fix-cupped-inserts-using-uv-windshield-repair-resin-a-work-in-progress

You should always wax before Mylar. Maybe not critical in your case, but you don't want the glue to become one with what's underneath . The wax works at the molecular level. If there is any perceivable wax when done buffing, you have to much wax.