One of the best, if not the best part of Fallen Enchantress games is the exploration aspect with your heroes-- especially in the early portion of the game. I think this same concept can be brought into GalCiv, where heroes can act as ship captains, generals, etc. If anyone remembers the old Star Wars 4X space game, Rebellion, you had various characters throughout that gave certain bonuses in certain situations, and it really brought a lot to the overall experience.
In addition, heroes would open up the whole ground combat aspect of GalCiv, which I maintain is the single-greatest missing link with GalCiv 2. I never understood why ground invasion was so much of an afterthought, considering how much detail and strategic scope went into the space combat. A hero system seems like a great way to put more meat into the conquering of planets in GalCiv 3.