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There are some buildings that I can't figure out the purpose of. I mean University, Surgeon's college and (for the catholics) Military academy. They do not enable the production of any units, agents, offices, do not give any valour or morale bonuses. What are they for?
Military academy increases the discipline of the units. I am not sure but this could affect knights as well, so Catholics do win from this building (a little). But I don't think Byzantines gain much from building the Acdemy. University allows the Academy and the College. Some factions (Poland) have GA goal to build uni and it could be built for roleplay as well. Maybe it is a result of other factors but building of university seemed to increase the ruler's influence. I need to check this. College of Sergeants addsa a huge happinness boost (40 per cent).
Truly useless buildings are the the various kind of Courts when you play as the Byzantines. Royal Palace is the only valuable building of the line for this faction.
iirc palaces give titles for your generals so they are not completely useless.