In another thread, I called for the replacing the current leaders with institutions, with far more elaborate modifiers to their task and especially immortal, so we are spared the reshuffling every time someone kicks the bucket. However, to retain the personal touch individuals give to a game, I suggest the following:
Replace leaders with heroes (or champions or whatever). Heroes will be the ones to research anomalies and be picked for event chains. All heroes can basically do the same things, though of course some are vastly better at certain tasks than others (for researching the strange radiation from a black hole, you should rather send Spock than Neelix). Besides researching anomalies, they could also give powerful but strictly localized help, like cracking down on crime on one world, infiltrating a hostile planet to aid the planetary bombardment etc. Should Stellaris get more elaborate diplomacy and/or espionage options, these heroes could also come to shine there. Perhaps, instead of the generic randomly generated leaders, we could take notes form Master of Orion and have pre-made leaders, each with his or her own traits, perhaps some would only be available (or not available) to empires with specific ethics or civics (Space-Genghis-Khan will not join you if you are pacifist, while Space-Gandhi requires it).
Regardless, much like now, I would give these heroes traits and skills. Anomalies (or other tasks) could also have suggested or pre-requisite skills. An example: there could be a medical skill heroes could posses. Now, some anomalies have a blue medical symbol. This means that heroes with the medical skill will research it, say, twice as fast. Another anomaly might have a red medical symbol. This means, only heroes with the medical skill can research it in the first place.
Replace leaders with heroes (or champions or whatever). Heroes will be the ones to research anomalies and be picked for event chains. All heroes can basically do the same things, though of course some are vastly better at certain tasks than others (for researching the strange radiation from a black hole, you should rather send Spock than Neelix). Besides researching anomalies, they could also give powerful but strictly localized help, like cracking down on crime on one world, infiltrating a hostile planet to aid the planetary bombardment etc. Should Stellaris get more elaborate diplomacy and/or espionage options, these heroes could also come to shine there. Perhaps, instead of the generic randomly generated leaders, we could take notes form Master of Orion and have pre-made leaders, each with his or her own traits, perhaps some would only be available (or not available) to empires with specific ethics or civics (Space-Genghis-Khan will not join you if you are pacifist, while Space-Gandhi requires it).
Regardless, much like now, I would give these heroes traits and skills. Anomalies (or other tasks) could also have suggested or pre-requisite skills. An example: there could be a medical skill heroes could posses. Now, some anomalies have a blue medical symbol. This means that heroes with the medical skill will research it, say, twice as fast. Another anomaly might have a red medical symbol. This means, only heroes with the medical skill can research it in the first place.