A small problem with Master and HQ Guildhouses (might be moddable, but it's a bug imo anyways):

Master Thieves' Guild gives a global +1 bonus for spies, but doesn't give the city-specific +1 agent bonus that the basic Thieves' Guild does. So, as a result, the best spies will be built in a city with basic Thieves' Guild (you have to have the Master Thieves' Guild in some other city), as the agents built there will get BOTH the local guild bonus AND the global Master Guild bonus.

I'm quite sure this same irregularity appears with other Guildhouses with global bonuses too (Master Merchants' Guild etc).

The solution would be to add the local bonus to the Master Guildhouses and Guild HQs in addition to the global bonus.