You definetly hit the point with
Beacons (permanent / non permanent → loss of property/ lootability of property, size, flexibility, ) and
Guilds / Task Forces (progression, anti griefing ideas, non abusability). I recommend 2 systems here, because there are intentions about them, that do not fit together:
Guilds should compete for world dominance ↔ join as many guilds as you want to be able to work out diverse projects in “smaller” groups.
Further Topics:
Progression model (linear/exponetial, finite/infinite)?
Achievement model (missions, rewards)?
Energy systems for machines of every kind. i.e. electricity/energy and water pressure. The idea of water power i introduced in topic:
post 35/36. other potential systems?
Use of water (just environment or interactive?) I personally like pipes by the way 
lowers the complexity.
Titans and temples (Expectations, ideas)? Especially temples still need a concept.