Both sounds reasonable!
We actually use limits on national units and unique units quite excessively in Realism Invictus. Also, there is another type of limitation there, and this is for all units: units of the same unit class have increased production costs. E.g each knight-type unit cost is increased by 5% of the previous one: 1st is 100%, 2nd is 105%, 3rd is 110%, 4th is 116%, n. is 100*(1.05^(n-1))%). It actually promotes mixed armies, both for the AI and the human player.
I'm not really sure if I want to go in that direction for RFCE, it's a huge change on gameplay. Will have to think about the possibilities a little more.
Also the potential Ghulam route from SoI, in that each company unit also has a cost of 1 on top of the unit cost to discourage mass production.
And consider giving the company units the same penalties as knights and lancers when attacking cities - at the moment they don't have those which just makes them more OP imo.