Why not give each estate 3-5 slots depending on the size of the region and allow them to build same buildings? Make the bonuses of each buildings not very significant.
Maybe each time you build courtier's office or something, you will improve the estate efficiency by 5-10%? Make it simple and help knights with estate as large as 50% improve their efficiency.
I also dislike storing units. We can already do something similar with our militia units.
I'd rather you give each estate only one slot and make the building really significant. That way you really need to think about what to build, and this will create diversity in regions.
