Stuff using BUILT_IN. Spinal mount Death Rays, Armageddon Launchers that are bigger than a Frigate and blot out the sun. Weapons that transport the target into Phased Space, doing no damage, but shoving them back 1000 su. Basically, stuff that's weird and you can't mount it elsewhere, so the ship can be balanced around it- the Monitor, only in terms of offense.
Ships that actively effect the ability to see on the battlefield. Apogee used to do that; I want to see ships that do that in reverse to the enemy, or that can suddenly clear the Fog of War over large areas, or can blind missiles or give fighters false orders for 30 seconds or whatever. This is an area where it seems like there are lots of niche ships that might be fun.
Destroyers that can actually be late-game player ships. I think piloting Cruisers and Capitals is boring, personally, and ever since stuff like Hyperion / Tempest were nerfed into almost irrelevancy for anything past early midgame, I've missed having things that can fight, kite and dodge, but take some hits without wilting. I don't really care if it's a super-Destroyer that costs a lot deploy or whatever- I want stuff that's fun to fly and can kill things well in player hands, not yet-another group-juggling exercise that lumbers along. Preferably with a gimmick System that the AI won't really "get".
Stuff that's not boardable and is truly terrifying. [[REDACTED]] is scary, because it has a cute gimmick, but I want to see stuff where I'm pretty sure nobody can beat it... then see somebody's silly thing that can. I feel like Derelict leaves too much on the table; it's meant to be like an easy [REDACTED], which is supposed to prepare you for [[REDACTED]]. IDK, I guess I want to see something that looks like a mountain of used copy machines with engines or Doritos served up with a Spicy Pizza Slice. Something that makes me go, "uhhhh, what just happened to my fleet, lol".
Utility ships that have a point on the battlefield. I built repair-ship mechanics... 9 years ago. We still don't have them in Vanilla today. Ammo-reload vessels, ships that deliver magical boxes that restore fighters or CR, ships that provide movement buffs, better ranges, inflict debuffs on enemies... the list could go on and on. This is maybe the biggest missing thing- that the utility vessels are meant to be seen, but not used, is a problem. Part of it is that the ones that are in are so horrible in a fight that players naturally conclude that they should never ever be used that way.
I still think my in-game capture system was more fun than a dice-roll, too.