I use Nike Lance shoes (carbon sole, leather upper) which breath very well. I never experience hot spots but feet quickly suffer if you have low blood sugar. Extremities like the feet, especially when kept in one place will start to feel strange if you have low sugar levels so make sure you have plenty of sweet stuff in you before a long ride.

Other than that, I agree with these guys, try the shoe loosening business, that may work for you and if not, just play about with how tight each fastener is when you ride. You will find a comfortable position!