Muon, I think it's not surprising that a conservative justice thinks differently about the Constitution differently from a law passed a few years ago.
The Obamacare case was about statutory interpretation.
The gay marriage case was about substantive due process and whether or not you view LGBT people as equal human beings.
In both cases he was writing in a way that seems to oppose to judicial activism by means of preserving the maximum role for the legislative process. After reading both opinions and the main dissents, I think he sees the whole question of judicial activism differently than his colleagues on either side. It seems like a blend of modern ideas and older ideas that had fallen out of favor, and clearly not the way Scalia sees it.