I'm not quite sure about sorting of FF. Some of them seem to be misplaced - for example Diego Velazguez, one of the late-game military FF, provides merely 4 cannon regiments, while cheaper Dom Pedro I gives outstanding promotions (minuteman, veteran) for all gunpowder units and +50% great general rate.
Good example of FF positioning is Jean Talon - he provides very good food production boost and is thus extremely useful, but only at the beginning of the game, simply because you can obtain 1 expert farmer and 2 fishing boats very easy/cheap later on. My point is, that this rule works for all FF: early ones should give you some temporary advancement (free units - experts, soldiers, natives, ships), which helps you develop your small colonies. Trick about them should be choosing, which ones will benefit you the most in your current game, depending on factors like territory or natives. Mid-game FF should be about enhancing your colonies, while still providing some units, although more powerful or in greater quantities - Francis Drake, Juan ponce de Leon, Chief Powhatan and all "+25% to 'good' production" FF come to mind. Late-game should be all about empire-wide bonuses: additional goods from certain buildings (like Henry Fox & crosses), free buildings (Sor Juana & chapels), double-production speed or free promotions for military - it's the time for finishing your combo (created from your leader's traits and chosen FF) and preparing to face the King.
Or maybe FF are as you wanted them and I'm wrong?