1. James actually smothered his wife to death because he resented her for wasting his life.
2. James also killed his wife because he wanted to end her suffering.
3. Pyramid Head, is not actually a simple punisher, but the representation of James' sexual repression and violent urges.
4. He actually believes that he is dead and Nautilus is the afterlife.
5. Relatedly, James' comment about Ratchet looking like an overgrown cherub is not far from what he actually thinks of the Docbot.
6. James no longer keeps track of the day/date/time.
7. He rarely eats anything anymore, due to the lack of hunger in Nautilus. Even twinkies.
8. He now prefers the hood of a car to a bed.
9. He'd rather practice his medical studies than be forced to socialize.
10. Despite his chosen profession in Nautilus, his dwelling and his choice in company... James despises doctors and medical staff deeply.