In the images you posted if you check out the performance meter you can see that pathfinding was taking all the time in the first image, and Lua is taking most of the time in the second. If you could upload the save where this is occurring to the thread I have linked below, @ponder (and team) have been working hard to make performance improvements in large games.
http://discourse.stonehearth.net/t/epic-gigantic-a14-saves/19524?u=jomaxro