I think the Industry tree is kind of a problem, cause I feel like it's pretty much mandatory to take logistics skills.
I completely disagree with this statement. In my experience money is never an issue in Starsector, and you can always carry more supplies/fuel/crew, always free to add extra ships to carry goods or have a stacking survey discount, and colonize as may worlds as you desire.
For example, even if I handicap myself in early game (no Galatia stipend, no commission, no black market trading, no raiding, etc.) to have a rough start, yellow skills feel "okay" at most, usually just "meh" or "why would I take that instead of something that gives my fleet advantage in only thing that presents any challenge at all and cannot be solved by adding more stuff to your fleet, namely combat". Usually an answer to every logistical issue early-mid game is "bring more Shepherds".
And if simply playing a regular game, they become complete and utter garbage. Want more storage space, loot, repair rate or burn speed? Bring an extra specialized vessel or, you know, install a few hullmods. Most of them are rather cheap in OP and can be installed on civvy ships.
Although Derelict Operations exists, I must admit, and that thing is absolutely nuts if properly built around. But that is rather extreme case of specialized playthrough based on metagame knowledge and isn't fun for most players.