A lot depends on player experience because combat has a steep and long learning curve, but a generic gunship under "medium" player control does about 3x the AI without any cheese. Early game I'll just grab the tutorial hammerhead and elite ballistic mastery + crew training (one for me, one for my fleet) and expect to do the majority of the damage for a long time. The value also depends on the player scaling their ship up. I really enjoy flying wolves/medusa (I find the phase skimmer very satisfying/fun), but at a certain point I've got to switch into something bigger or the player contribution/skills start getting wasted.
True "playerbait" ships are insane though. More like 10x what the AI can do or more.
The fact that this is true, along with the fact that you can do a whole run just as a commander, never actually piloting combat ships yourself, is one of the best things about this game.
Back to the original topic, I kinda feel like there should be separate skill trees for each of the major game layers, too:
1. Piloting
2. Leadership
3. Logistics and Engineering
4. Realspace and Hyperspace Navigation
5. Colony Administration
You'd get points specific to each tree, and you specialize in certain trees to get an extra point or two. Perhaps each tree could have different sub-categories (low-tech, midline, high tech?), and if you could get additional bonuses for having 5 midline skills, for example.
People have expressed balance concerns, but splitting them up would actually give you
better granular control over balance - instead of allowing a player to dump a pool of points all into piloting (or w/e) and becoming this absolute game-wrecking beast, you'd be more limited.
The current system is good, I don't think its crying out for a rework; this would be a low priority for sure, assuming it didn't just end up being worse.