Use a set screw in the middle of the hinge. This pin goes into the hinge and through the hinge pin so the pin can't be pulled out and the screw isn't accessible when the door is closed. Security hinge sets come with a hole predrilled for this purpose or you can drill your own hole for a screw to fit into.
Slide crimped hinge pins into the hinge to make the pin harder to remove. The pins are longer than the hinge plates and the ends get crimped with a wrench or vice after insertion so they can't be pulled out. This makes replacing the door more difficult but the door will be more secure.
Add a chain latch to the inside of the door. The hinges are not the only vulnerability in the door and the chain helps prevent the door from being pulled open. Drill the chain holder into the door frame and the slide bracket on the door. The chain connects the two and makes the door tougher to bypass.