Giving the game some sort of sensor system could be interesting. Stars, nebulae, line of sight/proximity to celestial objects could affect it, perhaps. You could have research techs to increase sensor strengths in those environments, and the scout could become useful in an attack fleet as, logically, it would have the most sophisticated sensor systems.
Just, for the love of god, don't give grav wells fog of war

It's far too common in games and it feels very artificial in space. It's one thing in land-based RTS games to not know what the terrain looks like until you explore it, but space is space, there's no terrain and not being able to detect anything on sensors doesn't mean the skybox should be all blacked out. Currently if you try to zoom in on a planet you have no presense in it will gradually fade to darkness and you won't be able to see inside the grav well, but you still see what the planet looks like, or asteroid, or whatever it is. That's as far as it should go, I think

idea 2: uncircular graw wells for "non planet" planets
Two thumbs up for varying grav wells idea for spacial anomalies/asteroids. There are some planets with lower/larger grav well properties, but it would be much more interesting to have a non-uniform well, then even the jump-in direction might matter