I have not heard of any way to toggle anything on/off on the main map, but there are a few I would like to see in addition to trade routes and shipyard sponsor lines,. I would like to toggle relics, resources, asteroids, anomalies, ships, planets, stars, just about anything each independently of each other, while viewing the main map in tactical mode, at least when zoomed out to the extreme.
I would also like to be able to see where ALL of my ships are going (auto pilot trail) via a toggle when trying to select a planet to send a colony ship. This would also be nice for rally points.
So many useful mechanisms from GC2 have disappeared in GC3.