Nice to know that some many games out there (that I haven't played ) do have characters too. I understand that Rebellion means Sins of a Solar Empire?
64-bits and all, I was thinking that the number of those heroes could be different depending on the size of the map. Five heroes, for example, could be enough for a normal map but for a super duper 64-bit huge-to-infinity map, that number would be too low.
The poor from where you can recruit (AIs would get their own one, obviously) would be composd first of members of your race(species or whatever) but as you meet new ones, new options appear in that pool. Aligment would condition that too (good Altarians don't get to use evil Drengin). The current number of employable heroes could be base on faction traits, researched stuff and "popularity".
I'd keep them quite simple. Even if there was tactical combat (fleet and ground), battles would be to big in scale to have them running/flying around by themselves. So gear may not make much sense despite it having some potential. Being able to level them would be ok though. And being able to specialize them further or maybe in other stuff could be ok too. Maybe Luke Skystroller beings as a hero taht gives bonuses to population growth but you later wnat to add some bonuses to ground combat. Plus also allowing to work with whatever you got instead of tirelessly waiting for the correct guy to appear in your recruitment window.
But in any case, nothing complex with tons of stats for each one. Portrait, name, race and aligment would be a must. From there, some skills would be enough. No Hit Points or Mana needed. Or resistance to lasers... If they are defending a planet that gets conquered, there would be a chance to lose it for good but if they escape, they would appear in another of your planets but unusable for X turns. For fleet battles or atacking planets, losers would have an even reduced chance of surviving. No hit points at all. Live or die.
I like that of using/abusing them with espionage related stuff. Not sure how "sleeper agent" could work considering than anyone else could be trying the same on the same guy ("You lost control of your sleeper agent" window?).
But yes, spies, admirals, merchants, researchers... So much could be done with them!