Barrdyn

Use a system similar to Eve Online. An enemy Company wants to claim your flag. They initiate the claim but it doesn't proceed automatically. The defending Company have 24 hours to set a time window in which the flag is vulnerable. If the enemy Company meets some pre-determined condition (such as killing all active players in that flag claim) in that time window, they claim the flag. If they don't then the defending Company keeps it. Failing to set a time window in that time results in automatic forfeit of the claim. Time window applies to any official allies, but not to third parties. Outside the time window, buildings are invulnerable.

Wild animals certainly shouldn't count as crew. Livestock limit integrated with existing weight limits seem fine.

Clearly you are incapable of understanding my satirical post, so allow me to enlighten you. I, a pirate, sit just off the Freeport with a galleon, blowing up every player ship I see, merrily looting their resources. Not allowed to enter Freeport as a pirate? No problem, I will have a vassal Company of one or two people unconnected to my pirate Company who shall sell everything for me, and return with the proceeds. Double cross me? No problem, I will sink them and take my gold. It isn't "non-visionary", it is "I've been around long enough to tell you exactly what will happen."

*sits at Freeport with galleon, blowing up any passing ship and taking their resources to trade for gold* You need alternate gold income for that reason alone.

Build a ceiling, hit T.

Agreed. I think they should be a gateway to the islands which spawn the mystical creatures, rewarding clever play and teamwork for killing them. Perhaps set spawns in lawless regions, in lairs that do not permit building, protected by higher level animals of the same type. Give them some kind of unique resource which can be obtained from skinning the body.