Time to overheat is incredibly for most ships. For some ships main thrusters seem to overheat faster than maneuvering thrusters. Is this intended?

It is a consequence of the main thrusters generating the most heat because they have the most power. Their current overheating system is only based on heat right now. They are generally not happy with the system right now because it is very linear in the sense that you press the button and it overheats. They want heat to be more of a long term consequence, and the managment of energy to be the short term consequence.