Aside from his wings, he was fully regenerated at the beginning of Prime 3 thanks to phazon, but he had to get some cybernetic parts again after his defeat on Norion. Not as much as he used to have in Prime though, which is why Proteus Ridley would be plausible
We know the suit is progressively "growing back" its armor plates after they were surgically removed in Fusion, but honestly I wouldn't mind if the suit stayed as it is in Dread with some organic parts permanently showing