Probably the biggest remaining unknown in the universe of Tiny Empires 3000 is the set of requirements for creating a guild. A Director needs a number of things, and that has been published. But a guild is still unknown territory.
One thought that has occurred is this: what if one requirement is to have a Board of Directors? After all, every corporation has a Board of Directors, so a potential Guild Leader could well receive the message "Before you can form an official guild of your own, you must have a Board containing X Directors".
In game terms: have this many of your direct subjects be Directors. It would be a very effective way of requiring a guild to have a minimum fleet size. Say you need five Directors, each Director needs at least 25,000 ships to have that title, so the minimum size of a guild immediately becomes 125,000 ships- more, in reality, since it would be unlikely that five Directors would have just barely the minimum amount required.
Add that to the possibility that much "guild business" requires a "quorum of X Directors", and you could have the perfect way to "de-activate" smaller guilds. It would also give a Guild Leader a motive to keep his or her Directors in the guild- if one of the Directors leaves to form their own guild, it could put the old guild out of business if they had only the minimum number of Directors required to do business.
At this point, pure speculation, and very likely off the mark... but it just fits together too neatly to be dismissed quite so easily.