It doesnt look nice when ships go throu base mesh, it would look better if ships flew over it like they fly above planets and suns.

Would it solve the problem if you could offset the base graphic below the plane of play?

except that station also fly above planets. so if your on top of a station on top of a planet, it would look really weird too. im not sure what the best solution would be. i guess we could offset the graphic and remove their code that make them go over planets. Will have to try that out to see how it look later.

Could it be possible to make stations be a physical block(IE, you bounce off it)? And make a docking ring around them that allows for players to slow down inside and dock?

The making Planets/Suns/Moons/Drones/Bases(Player) be under the 2d plane?

Dont like that either. How about just making either A: Your ship turns pure red and is always visible when covered by other models, or B: Other models become semi-transparent when your ship is beneath them?

I really think dropping some of the larger suns below the Z-axis, as well as space stations would be a nice addition. It would give a better feel of depth.

Your ship should pretty much always be higher on the z-axis than anything else, excluding nebula's and other intentional effects.

Making other models translucent when they overlap you might be a pretty good solution.