System Defenses
I mentioned these briefly in a post about "boss fights", which made me realize this post was a good idea.
There are some basic defenses that work well in this genre, and could be used in more than just boss fights if they were going to exist for those anyway. In the original SC you always fought on the same map, and a homeworld was simply unbeatable with unlimited ships and you had to warp away. System defenses could exist in populated systems that would still be fairly simple but more than just always being a 1v1 duel on an empty map.
Minefields. These are an area denial weapon that is more effective when covered by something that can attack ships attempting to clear the minefield.
Defense Satelites. These orbit planets, or starbases, or just sit in open space, and can be armed with any type of weapon or device you might dream up. They are effectively "mini-bases".
Basestation/Battlestation/Starbase. Various sizes of "combat military bases". The heart of the defense.
Planet based weapon. Fighters are common, potentially lots of them, but just like any type of base any type of weapon or device might be used.
It would be easy to make homeworld defenses unbeatable (and it would look cool, too), and then in other star systems these types of defenses could be used in more ways I could even begin to list here. It adds a lot to the game for so few objects to create and can be used to defend quest items, in boss fights, or just to provide various levels of defense at certain star systems for whatever reason.
Generally, minefields deny access to areas. DefSats and BaseStations overwatch minefields (maybe even a battlestation). Planet based weapons can provide powerful and unique effects to make the defenses even stronger (like the ship disabling Ion Cannon in Star Wars, for example). A Starbase would be balanced to be difficult to defeat all by itself using the players entire force and is the ultimate defense but a rare thing. These defenses would be designed with SC's nemesis balance in mind, so certain ships would be better at picking apart different parts of the defense. For example you might have one ship that can take out the DefSats from a distance and another that is good at clearing mines. Then a ship that is good at killing the weapons on the base, and another that does the heavy damage to take the base down but would have died to it's independently killable weapons that the previous ship stripped off of it. In a defended system the player would have to either avoid or kill the enemy ships while picking apart the defenses if he must defeat the defenses, or avoid the fire from the defenses to defeat the ship if that is his goal. Ships would keep respawning as normal until they ran out of them.
You could get a lot of use out of these few objects and make the galaxy seem more real with these very simple defenses. It would also make the player want to carry a mix of ships that allowed it to defeat defenses what the situation requires it. You don't always have to take down the defenses, sometimes they are just there supporting the ships you need to destroy to end the mission.