You can't copyright game mechanics, so you don't have to change from using a d20. All you have to do is:
1. Not claim OGL licensing (to be able to GSL)
2. Not be found to be infringing on the copyrighted material in the D&D Player's Handbook or other WotC products (to not get sued as a result).
Looking at the M&M 2e book, they'd definitely need to rework the first 10 pages heavily - not cut and paste the list of definitions from the SRD, for example, but reword them.
It's easy to be "scared of the lawyers" because of how litigious Hasbro is, but if you look at the relevant suits you'll see they've lost the ones where it matters - like, for example, the "Monopoly add-on" suit. And even the Scrabulous suit is being analyzed by legal folks to revolve more around whther they took trade dress or not versus the rules, even down to a high level of specificity.
http://mxyzplk.wordpress.com/2008/04/09/scrabulous/