I think I brought this idea up in IRC last week, specifically about military leaders and bonuses a player faction might gain on the overmap because of it. This is me expanding on those ideas a little.
Basically, each faction has a certain number of named "heroes" who boost various stuff in various different ways. This could be a master admiral, a sly politician / spin doctor, or a genius scientist. Each of these earn experience doing things they're good at and level up to gain new abilities - military leaders gain XP through winning battles, scientists earn XP by doing science, politicians earn XP by being sly bastards, etc.
Basically, there a certain number of levels (a small number - maybe about seven max) and at each level the character gets a fair boost to how they accomplish their task in general (research projects under a scientist goes +5% faster, for instance) and they also get to choose one perk from a set of five, la little like Fallout. this might give them a substantial boost to a stats in certain circumstances, or give them a new ability like an admiral being able to get more Fleet Actions for his fleet for one turn at the cost of a reduced number of Fleet Actions the next, or to give a Scientist a random chance to make some kind of breakthrough that adds some kind of added benefit to research, or a Politician being able to launch various initiatives to make his planet happier / more productive / easier to defend etc.
Buuh more stuff to be edited in later. okay here's a little more.
Basically, this all makes scouting and intel a little more important, as if you don't know what an opponent's leaders are capable of your opponent can gain an advantage. However, another idea I had for level-uppable characters would be spies / assassins, who can infiltrate enemy space and dig dirt on faction movements but also officers and their special abilities. They'll gain XP through not being caught and pulling off ballsy super-spy stuff through perk abilities. If you manage to get your spies in close to an enemy leader, not only will you manage to know what he's capable of, you'll also be able of interfering with faction operations that are being led by that officer, and, if you take the right perks, might be able to assassinate him.
All characters under this system are capable of being killed in one way or another. Politicians and scientists can be killed or captured in an attack on a planet, spies can be executed if caught, all can be assassinated, and all can die if they're on a ship that buys the farm.
As for where these heroes come from, that's something I'm not entirely sure of. You'd probably start with two or three, the nature of which depend on your faction's background, and getting new ones might depend on fluff too - for instance, factions with Imperial backgrounds might have an academy on their homeworld that brings through new officers, or if you're a pirate or mercenary new officers would come in as you gained prestige through battle. Like I say, not entirely sure yet.
Maybe more to come, any ideas welcome.
I have to kill fast and bullets are too slow.