Right now, I feel the various categories for XOs aren't very interesting, and despite the low number of XO slots, you aren't really forced to make choices due to there being... three very generically strong and useful categories- Tactical, Technical and Warfare. Tactical has range boosts and some powerful damage boosts, Technical has speed boosts and flux boosts, and Warfare has range boosts, maneuverability and armor boosts. These are all quite powerful and generic enough to apply to everything. What if instead of these, there were three 'doctrines' which are, yes, generically strong, but also mutually exclusive with each other in the way which Starfaring / Piracy is, and more rooted in Vanilla's flavor. This would hopefully open up more interesting build choices and encourage players to take the other 'more niche' skill trees.
Doctrine concepts
Decisive Battle (Hegemony's preferred doctrine / Low Tech):
Range!!, ballistic weaponry, armor, keeping opponents engaged and getting that initial engagement. Hegemony (and to some extent Low Tech ships) *loves* doing one big, decisive engagement. Two fleets collide, one fleet emerges. Warfare has a lot of this in it already, but isn't it exactly, i think. Burn Drive exemplifies this doctrine, I feel.
Hit & Run (Tritachyon's preferred doctrine / High Tech)
Shields, speed, flux capacity & Active Venting. Also phase ships, though Phase Ships should probably get their own XO. Tritachyon (and to some extent High Tech ships) loves to be able to engage and disengage at will. Technical has a lot of this in it already, but, again, isn't exactly it. The Aurora is obviously the thing which exemplifies this doctrine.
Close Support (Persean League's preferred doctrine / Midline)
This one is a little trickier. The Persean League likes to have ships which support other ships, either via missiles or via long ranged weaponry(Vigilance, Gryphon), and other ships to keep hostile ships occupied(Falcon, Eagle). I'd advocate for Zero-Flux boost, missiles, and maybe some weapon output stuff(Sunder & Hammerhead). Tactics is... vaguely this? Probably also some defeat-in-detail stuff- the Conquest is, yes, good at Close Support and has a lot of missiles, but is also *the* flagship for defeat-in-detail tactics. Conquest is probably also the poster for this doctrine. Oh, if any of these should get that 'beam weapons deal hard flux damage', it should be Close Support, not Hit & Run.
...part of this is just making Speed and Range mutually exclusive instead of allowing players to take both. But I do pretty strongly feel that Smallcraft, Strikecraft etcetera aren't really competitive options compared to Tactics, Technical and Warfare. Starfaring is good, Piracy is interesting, I think those two are fine.
oh, it's also notable that the player can't get Industrial Planning with this mod.