Logistic and non-combat ships of one shade or another make up nearly a third of all vessels in Starsector. They come in all shapes and sizes and varying degrees of being able to defend themselves. However, at least in my experience, they so rarely make it onto the battlefield that I literally never mount weapons on them or spend OP on increasing their defense. They exist solely to increase fuel, storage or crew capacity and have the secondary effect of having enough OP to add in Surveying Equipment. As a player, I am not penalized for this approach but I should be.
Leaving your supply convoy completely defenseless is perhaps the easiest way to lose a fight before it begins in the real world. I know Starsector isn't heavy on realism but even a nod to striking your enemy's logistic capabilities could make battles more interesting and varied. It would also get 20+ hulls into the fight that weren't before, which means the defensive advantage a Tarsus has over a Buffalo might actually matter.
Here are a few scenarios (I'm sure none of them new) that I think would add some variety:
Protect/Attack the Convoy Scenarios
Guarding convoys or civilian transports is an extremely common mission type in other games so I can forgive an eye roll or two for even suggesting it. However, it would present an interesting challenge in Starsector. For starters, you do not have direct control of your allies so even if you gave them guard orders on a ship, there's no guarantee your fleet would do a decent job of protection. It would be frustrating to "do your part" as a player and still lose a mission because your AI allies failed. I get that.
However, I think gameplay opportunities open up when there are additional victory conditions beyond "kill the enemy." If the player is raiding a convoy, a victory condition might be "Destroy 3 logistic ships." That means you don't have to actually engage the defenders if you don't want to or if you're unable to. Having 2-3 Hounds or Lashers with SO dart around lumbering Dominators to blow up Buffalos sounds like fun to me. It allows for more asymmetric warfare as an attacker or defender. Even if you have an endgame fleet, raiders might be desperate enough to attack your logistics train. Not having quick-responding Frigates or your logistic ships properly armed means all those ships get destroyed.
In these scenarios, maybe the battlefield rules change a little. Convoy ships are "on rails" and/or are in a defensive wedge formation and the battlespace is a bit more confined. Maybe Defend orders are more strict or the AI behaves a little more aggressively as defenders. The point being, it wouldn't just be two fleets smashing themselves against each other and the outcome of the battle would depend more on flexibility and maneuvering than brute strength. Likewise, maybe only certain ships can participate, namely Frigates.
Spoiling Attack
If an attacking fleet has a +2 burn level higher than a defending fleet (excluding Sustained/E-Burn bonuses) or cannot be detected at a certain range (TBD), a "pre-battle" option is given: Spoiling Attack. In this scenario, the attacking group forces all enemy logistics ships onto the battlefield. Due to the nature of this quick attack, only a small portion of the attackers or defenders are actually involved (~30 DP) and it is limited to Frigates and Destroyers only. The defender's logistics ships do not count against the DP cap. The scenario is also time-sensitive depending on the size disparity of the attackers vs. defenders. If the defender's fleet is much larger, the attackers only have minutes before the big guns arrive. If the defender fleet is much smaller, the scout force has more time to do damage and score kills.
Destroying logistic ships has CR effects on incoming warships, which is the point of the attack. Destroying "supply" ships reduces CR (by some % TBD) and destroying "fuel" ships reduces top speed in battle. After the timer runs out (or the logistic ships are destroyed/retreat, whichever is first), the rest of the fleets are able to be deployed per usual. If a spoiling attack is successful, a much smaller force may be able to fight a much larger force because the larger force is crippled. Imagine a 120 DP fleet fighting a 240 DP fleet but the spoiling attack reduced the entire 240 DP fleet to 30% CR and 50% top speed. It would still be a hard fight, but perhaps doable.
Alternatively, perhaps this is a Story Point-driven maneuver so it isn't too commonplace. That said, whatever the initial conditions are to allow this to occur should be possible with a carefully tailored fleet. A fleet specialized for speed (Navigation, Augmented drives, etc.) or for low sensor profile (phase ships, Insulated Engines, Militarized civilian ships, etc.) should be able to pull this off more frequently/effectively.
Where this gets tricky is that the player cares about their logistic ships while enemy fleets do not. That is to say, factions and enemies will just spawn more while the player doesn't have that luxury. Losing a single logistic ship to one of these attacks is a major blow to a player, perhaps putting them into a death spiral, so spoiling attacks on the player would have to handled well. There needs to be enough of a threat to punish a player for neglect but not so much that they're always getting raided by gnats that were previously never a threat.
Overall
If you notice a trend, Frigates and Destroyers are in the spotlight as well as the Logistics ships themselves. Cruisers and Capitals would not take part in these scenarios (the in-game reason is they just can't react in time) so going All Big Ships would have disadvantages by end game. It keeps Frigates and Destroyers in the mix as useful additions to the fleet and it may even make you want to put Officers on them solely for the purpose of attack/defense in a spoiling maneuver.
But more importantly, it gives the player meaningful choice in their their Logistic ships. There is currently no reason to pick a Tarsus over a Buffalo right now because the Buffalo has better capacity and is cheaper to maintain. However, the Tarsus has 4 guns on it, decent armor and Burn Drive to escape while the Buffalo has just a Small Energy, poor armor and Flare Launchers. The Tarsus is far and away the more survivable option if the proverbial crap hits the fan. Likewise, combat freighters like Wayfarers, Shepherds, Cerberi, Hounds, and Mules (Gemini and/or Ventures?) would be included in these Convoy/Spoiling scenarios by default. They sacrifice cargo capacity for being able to truly defend themselves and that might mean I choose them over pure stat-sticks like Buffalos or Colossi.
Some might see these kind of additions as being a nuisance or at least a slowing down of fleet actions if the optimal way to play is "Spoil Attack every fleet." The same could be said if your endgame fleet could be raided by 30 DP pirate fleets: it's the equivalent of the much-reviled "babysitting" of colonies from punitive expeditions except now for your own fleet. If it were overdone, I'd absolutely agree. However, I would want scenarios like these (or others like them) to be more of a "sprinkled in" rather than a core mechanic. Unless you were to make a highly specialized fleet, performing spoiler attacks should be fairly rare or at least a very intentional gamble. Likewise if the enemy tries it on you. Being paid to protect convoys, on the other hand, could be a common mission type that would allow small fleets to make money early on while also engaging in larger fleet actions. Heck, you might not even be protecting logistic ships but adding a mercenary component to larger fleet actions where a particular warship has to survive.