suggestion: 1 champion per stack
So as I was reading about the desire to create more of an intertwining between your empire and your champions. What if by default, you could only have one champion at a time per stack of units? I think you would be forced to create more units, which would in turn force you to build your empire and research tech to more directly affect the outcome of your army strength. There could even be buildings (probably requiring a high level city and/or a tech) that would allow you to add a 2nd or 3rd champion to your army. Since you may be having more idle champions, add more traits that affect your city, and give xp for governing a city.
Also in order to purchase decent armor or weapons, you would need a forge, weaponsmith, armorer, etc depending on the grade of weapon/armor. Alchemists add potions, scribes add scrolls, why not the same kind of linking for weapons, armor, and accessories? Your town could get you your bread and meat to regen health, your fortress gets you your advanced mundane armor/weapons, and your conclave gets you your fancy magical stuff. You could even require dual techs/buildings for some stuff. In order to make an uber magical cold enchanted longsword, you first have to be able to master the creation of a regular longsword.
Just a few thoughts, that I think could be worked into the game at some point, or even a mod.