A couple of things to make space "less empty"
Military outposts: a more limited version of a military base, usable on "class-0" planets. Grants sensors area, combat sensors (bonus defensive/offensive) over an area
research stations: grants a small amound of research, sensor area, usable on "class-0" planets
Mine field: left from earlier times, causes damage to passing ships. Invisible, discovered to the player if a ship triggers a mine. medium to large area. Revealing the field does not disable the field (reduces damage caused)
Mine field (owned): deployed by a player, causes damage to passign ships except for the player (and allies)
Space anomalies
Distortion fields: causes random effects (reduces or disables defenses, increases evasion, slows down). Invisible, limited area
Nebulas: causes random effects (reduces or disables defenses, increases evasion, slows down). Completely visible, large area
Gravitational Wells: Invisible, if hit, causes damage, speed increase if moving towards the well, speed decrease if moving away. limited range
Sensors:
Better sensors decrease effects or completely disable effects making the anomaly visible (to the player)
Only a few anomalies can be seen at the start of the game, better sensors make them visible
Mine fields can be detected with advanced sensors