I'd be very curious the amount of players that invest in combat, and fly their own ships, versus those that don't and use auto pilot.
Do players who pilot their own, feel investing in combat is required? as someone that uses auto-pilot 90% of the time or more. I wonder if its because I skip combat, and go full manager, that I feel so horrible at actually piloting.
I'm inclined to think combat, and all the "piloted ship" skills should be separated, and in their own tree.
make that combat tree, have skills that focus on frigates and destroyers, versus focus on capitals and cruiser. have some skills focused on carriers. some on energy, someone missiles, some on freighters. allow the player to tailor their "self" perks to salvage, trade, stealth, or various kinds of combat. but, not have those self perks, compete with fleet and colony ones.
Piloting with a weak flagship (whether without ship skills or in a smaller class) is relying on player piloting ability to overcome statistical imbalance, because enemies have skills (and/or a better ship). This is doable, but its hard, and if a player hasn't developed a lot of ability yet (no offense intended: its a hard process and a lot of us have been playing for
years honing it) then its going to feel frustrating. As an example of the imbalance, take like a Hammerhead with one of your own high level officers + fleet skills, give it a 'mirror' loadout to the sim Hammerhead, and let them fight. The sim Hammerhead just gets crushed.
When someone is learning piloting, they can't overcome that kind of imbalance yet, and if they don't make their flagship strong they are going to get blown up or be stuck skirmishing instead of killing. When someone
has learned piloting they no longer need the strong flagship to win 'even' fights, so in theory they could do without, but... if someone has learned piloting to that degree, then what they can
accomplish with a strong flagship is huge, so its worth taking them anyways from a power perspective (and from a fun perspective, players who learn to pilot well often just enjoy flying a strong ship if they aren't doing a special challenge run).
Making the flagship moderately strong in the early game doesn't have to be personal skills because there are some really fantastic fleet boosting skills: early game when the player is piloting a frigate, wolfpack tactics + crew training + coordinated maneuvers (if you have at least 1 officer) is simply better than personal skills AND applies to all ships in the fleet. Wolfpack drops off in effectiveness for destroyers and then entirely for cruisers+, while for slow big ships coordinated drops off, so while this combo is very good early game, more is needed later (unless the player just goes Hyperion/afflictor murdering which is totally viable). But for beyond the early game, there just aren't that many fleet boosting skills that apply to the player flagship, so fleet boosting skills only get the player flagship so far and the next step is the personal skills. They don't have to be in the combat tree (both industry and tech have 2 strong personal skills, even if they are dependent on the ship type for energy weapon mastery and polarized armor), but the combat tree ones are good and stack.