AI:
Somebody already mentioned missiles that try to intercept rather than just chase. Absolutely. But still, let people use the old missile behavior too. Just add it as another type of missile AI to choose from. Maybe get creative and add some new behaviors too.
Redesign AI completely. Instead of just x number of set behavior types for NPC ships, give them strategies instead on how to defeat their opponent, based on what their opponents do. Have each AI assign its opponent an enemy type.
For example, if I am an AI fighter ship, fast and maneuverable with forward facing light weapons, and I'm up against another fighter, I will attempt to follow it and shoot it with those forward weapons when I'm really close. If I'm up against a large carrier or battleship, I will swarm fellow fighters and attack en masse firing my weapons at my longest possible range and try to stay out of its field of fire. If I'm up against a bomber, something that has a strong frontal attack but maybe can't defend its rear too well, I'm going to try to outmaneuver it and stay behind it. My behavior should change based on my opponent, not on my own ship type. My reaction as a fighter will be different against these types than if I was a different type of ship. If I was an AI capital ship, I would choose to slog it out against another capital ship at long range, run away from heavy bombers, and chase after weak fighters.
Decide what Opponent Type a ship is right there in the ship resource, but for the player's ship, be a little smarter and assign a type based on its armaments and outfits, or perhaps even the player's behavior. Then, match those Opponent Types with different Strategy Types. Intercept, Chase, Swarm, Stay at Range, Get Behind, Run, Call for Help, and so on.
The benefit of an Opponent Type/Strategy Type system instead of an AI Type system, is that it allows for much more interesting behaviors. A lightly-armed freighter might decide to chase down and kill a weaker fighter, but as soon as a larger pirate ship shows up, or maybe a bomber-type ship, the freighter runs away.
Systems:
Moving planets around based on the time of year is probably not that useful to many people, but it shouldn't be too hard to implement and some people may find it useful so it's worth considering. Give it an orbital period in days and a starting position. It'll use the starting date of the game and do orbits from that point around another spob in the system or 0,0 (null spob). They'd be able to orbit either clockwise or counter clockwise based on another setting in the spob. I wouldn't make it any more complicated than that, such as ellipticals.
Remove asteroids, interference, and murk from the system resource, and instead add them back in as objects like spobs, that can be placed in the system at particular coordinates with particular sizes and shapes. Circles, rings (with a given width), lines (with a given width), and system-wide areas can then be added to create much more interesting system features. Imagine an actual asteroid belt, instead of a system-wide field. Imagine interference given off around a particular spob but not elsewhere in the system, or murk found in just one part of a system obscuring a wormhole. Interference and murk would be easier to have regions for, and asteroid pathing might have to be adjusted somewhat so rocks don't stray outside their regions, but it would be worth it to get all three to no longer be just system-wide. Let people add 4-8 asteroid regions, 4-8 interference regions, and 4-8 murk regions and place them exactly where they want them.
Other than being pretty, imagine the tactical and storyline benefits to regional system hazards. A xenophobic planet or one undergoing a revolt might use jammers to blanket the planet and nearby areas with interference. A fighter being chased by a missile boat might duck behind an asteroid belt or dive into a murky nebula to hide.