Idea is to replace individual promotions with Military Doctrines, which would be promotions applied to units of certain level (green, tried, veteran, elite) empire-wide. Doctrines are created with Great Generals and hosted in military buildings (just like great works). E.g. Barracks for level 1 doctrines, which give bonuses to level 1+ (tried and above) units, Armories for level2 doctrines, Military Academies for level3. Pentagon or West Point also may have doctrine slots.
So there will be something to do for those excess great generals. Btw GGs may also have levels (like in my Commanders mod for civ4) so having a higher level would allow to create a superior Doctrine. GG promotions may help certain unit types so when your army upgrades, an old GG will have little use on the battlefield and should be better spent for a MD.
Individual units may still receive "occasional promotions" (like in my mod for civ4) which would be rare (depending on the chanse of surviving combat).
Military units also should be more expendable so the player could not conquer the whole world with his initial army of 5 units. This means more fragile, easy to die. There should be situations where the player have to sacrifice units (maybe even elite) to achieve tactical goals.