I too have wondered about this subject...
I agree with the push to increase the cooldown with throttle reduction and/or engine off. This added level of complexity to the game can only help, and its not like it really affects those who wouldn't do it all that much. Somebody could continue flying the way they currently do (bawls to the wall) without noticing any difference. Alternatively, they'll learn to conserve their WEP, manage their engines, become better fighters and feel more accomplishment, while overall improving the quality of the gameplay.
Meanwhile, I can see both sides of the arguement on the idea of having an engine overheat... While I personally would love to see the engine overheat and then explode, catch fire or seize up, I understand how this MIGHT increase the number of button presses one must do. Alternatively, a knocking sound could kick in at the point where the engines WEP currently cuts off and that could be a cue that you should turn off your wep. Even if this does kick in, then one could STILL choose to push the engine just a bit harder, if they need to and risk damaging it. To me, this would GREATLY increase the realism and make it a lot more interesting from a fighters point of view without really changing gameplay for some (most hit the WEP off and on anyway).
Meanwhile, stuff like cowl flaps, mixture, etc would definately increase the amount of micromanaging that goes on in the cockpit and I can definately see the arguement against them. The previous two points however seem very VERY valid in a WWII Combat simulator such as AH. Especially when one considers the amount of times engine trouble really played into the outcome of a battle. Those two little tweaks would go quite far in immersion and realism I think without increasing the learning curve.