Apocalypse wins: he can manipulate his body in the subatomic level so he can change the chemical elements in it creating complex machinery and weaponry; he can also borrow mass from another dimension and alter his denstity and size. Whether or not he is portrayed as knowing how to use this power effectively is a different matter.
MMH can only manipulate macromolecular polymeres within his cells, rearranging their structure.
They both can phase through solid matter.