I'm a game developer and I know it is extremely non-trivial to add a major resource category to such a complex game. (did you mean to suggest the code base was even available to modify?)
Just for fantasy's sake though, I'm quite enamoured with the elite manpower idea and I'd like to expand on it. Think of EMP as a "quality" resource. This quality should be selectable for both new formations and formations under repair.
The trade offs around quality are specific to the present conditions of your country. If you have high industry, moderate manpower with high quality like the western allies, you might want to build up airpower (assuming that is fixed to become more effective). As Germany, with medium industry, initially high manpower with high quality, it makes sense to build more elite land units. Soviet Union, with high industry, high manpower with initially low quality, will want to sacrifice quality to build a large number of land units. Japan is in an interesting position with medium industry, medium manpower of medium quality. It is forced to fight both the land war in China and air/naval war against USA. It has little elite manpower to spare for elite land units such as armor, and in fact will be hard pressed to repair its air units with high quality manpower.
Elite manpower is also great for modeling events such as the Great Patriotic War. The Soviet Union should start getting its EMP really after it goes to war with Germany and starts losing. Soviet effectiveness would then increase smoothly over the first 2-3 years rather than as a one off event.
Another use of EMP might be to model the decline of Nationalist China against the rise of Communist China. Nationalist China expends what little EMP it has fighting the Japanese, while the Communist ideological advantage gives them relatively more EMP. A small number of highly effective mountain units give Communists their mountain redoubts to start with. Once they capture a few provinces, they make better use of the local manpower than the nationalists did, and the whole thing just snowballs from there...