A millivolt system should operate and maintain the heater fine without having to relight the pilot. The only problem with a millivolt system is they are sensitive to how far the wire to the thermostat goes. You are working with such low voltage, that if you have excess wire, sometimes it will drop the voltage too low to work. On a pool heater however, the thermostat should be right there on the inlet water line and should function fine. If you are having a problem with the pilot going out or the gas valve not cycling consistantly, you can change out the thermopyle and it should work with no problem.