I do not know if any of this has been suggested, but for the civilian leaders:
1. Each system have a governor for the entire system and passed down a fraction of his abilities to each colony in the system.
2. A empire/federation/ leadership position for all systems. Under would be the sector Governors, the system Governors and the planet Governors. The tile of the empire wide leader could be determined by the empire theme.
3. The empire wide leaders could have a cabinet, Minister of war, industry, science, mining, terraforming etc.
I realize this would be a lot to add.