Something of a place for really basic balance/gameplay issues with the game. The type that could be overcome with simple tweaks.
1: Atropos torpedoes are simply lacking. For 6 OP, I get something generally worse than a Hammer (2 OP). There is just no reason for these torpedoes to be as bad as they are. It would be nice if they at least had more HP than normal torpedoes, granting them some use.
2: The Hound and to a lesser extent the Cerberus are just sorta pointlessly bad. Without shield generators, they need more armor or more something to really compare as viable ships. If these were particularly cheap to maintain or purchase they might even have meaning, or even if shielded cargo was important these days, but as it stands they are kinda flatly bad. Makes fighting (D) versions of them from pirates feel particularly like punching children.
3: Civilian ships in general - Shuttles/Liners/Troop Transports/The Atlas/Larger Tankers do not create interesting and meaningful trade-offs, they are just generally bad. Part of this is how the economy works, but in general the issue is that you can have a whole fleet of combat capable vessels that all can carry a meaningful amount of cargo, or you can have one giant cargo ship that slows you down tremendously, provides no combat utility, and isn't even cheap to maintain or purchase. The scales of advantages these ships provide need to be reworked such that they are interesting choices rather than really bad ones. Simply buffing their cargo/troop/fuel capacity might be sufficient. The disadvantages these ships often have are very large, it seems only reasonable that their advantages might be big enough that you would ever decide to use them.
4: (D) Hulls. Currently they are a minor price drop for a massive disadvantage. The easiest trade-off is what Starsector+ did, just reduce their maintenance/deploy costs as well. Make them feel like you have a budget version of the real ship.
5: Phase ships are mostly just annoying to face. Not exactly a balance issue mind you, but with instant re-engage and long duration cloaks it simply takes too long doing nothing to kill them. Even a half second of delay to cloak, or a flat flux drain when initiating it, would make them remarkably less annoying.
These are the ones that come to mind for me immediately. By all means add some if you want, there are like many more of these simple sorts of issues with very real solutions.