Well, I really hope we use heroes, but I agree that the FFH2 system would be to focused on heroes, as the mod itself is focused in high specialization and few, but strong, units. We could use a similar promotion system to make the heroes unique, giving them special habilities (even "magic"), and make them world units, but we should have heroes more alike standart units (even weaker, as they are a single person, but useful because of their skills).
By the way, how many heroes should we have? We have 18 civs, but I don't want to make heroes exclusive for one single civ but rather to its race, and also some heroes available for all factions (except perhaps The Shadow).