It would be great if the game drew grids versus dots for coordinates in similar fashion as ST4X, but each dot in the cell could be turned off. The grid color could be best on controlling government and dim for deep space.
My proposed ideas are geared towards taking a galactic sector and dividing it up into many playable maps (aka systems) . Systems are typically controlled by a government, but different governments can have an outpost in a system, establishing a foothold. Some planets or spacestations could even be controlled by independents, to include asteroid belt or comets (future encounters).
Game play would allow one to slowly expand beyond a system. The travel within a system is similar to how it is now (legacy green dots), but differs in map size (obviously). You see a sun or two with planets, moons, dwarfs, etc. But they orbit. The grid is polar which can make managing supplies more difficult as each time you enter the system, the planets may not be as expected. When you enter a system, the direction you enter determines where you start on the system.
When you leave a system, you enter deep space (legacy red dots) where travel is dangerous, exoplanets are unseen and hinder, and aliens roam. Travel is slow. Trade routes can provide a safer avenue and are less shrouded in uncertainty (missions to protect).
I would change not much else other than adding a fuel and water holds to ship stats, separating from cargo stats.