The colony master type player ...
Personally, I don't see why colony skills are considered tier 5 worthy in the first place. Doubly so for the ones in the fleet tree. How is +25% colony fleet size and +30% access on a colony you potentially don't even have better than an extra skill buffing all your ships with officers?
Just wanted to comment on this real quick: they're there because they're out of the way. The "real" top-tier skills are in L4 and I4. I don't think "colony master" is really a thing; there's only 4 skills total that have to do with colonies. And as you say, colonies are profitable without skills. You can pick a few skills there if you want them, but you're not obligated to in order to get the good skills in I/L (unless you're planning to wrap).
Which is a fair counter-point. How much are people "wrapping"? My assumption was that it would be a fairly rare thing. Incidentally - I'm now remembering - this is also why it felt reasonably alright to have Field Repairs and Derelict Contingent be contradictory, since the difference between I8 and I10 is basically just a "boring" colony skill.
So, to repeat, colony skills are in tier 5 so that you mostly don't have to pick them if you don't want to. And in some cases they have some non-colony bonuses so e.g. if you're wrapping Leadership, you can at least pick Ground Operations that boosts your fleet in some way.
I am a colony master player.
And the reason is partially because I like it, and partially because I often roleplay someone being absolutely "lawful", never doing smuggling, never betraying whatever faction I am comissioned to, etc...
When playing that way, you get much less money, so the colony money helps a lot.
And when you manage to make a really high powered "empire" you draw a lot of fights to your way, and end having those massive battles with tons of capital ships and officers on both sides, that make the default 400 dp maximum feel like it is way too low.
So yes, Colony Master IS a thing.
So what skills make sense for me? 1. all skills that boost colonies. 2. skills that let your colonial fleet shine, possibly even fleets that you are NOT controlling personally.
To be honest it feels to me you are struggling with the industry skill tree, not only it was developed last, you still don't know what you want out of it, it feels like it is half-assed colony tree, half-assed pirate tree, half-assed exploration tree, all at same time.
If you wanted it to be about exploration, you need to give back the skills to boost finding cool stuff.
If you wanted it to be more about actual industry, it need skills to boost production, lower tariffs, make easier to find trade contacts, etc...
If you wanted it to be more about being a pirate, it should have skills that help you smuggle things (for example more stealth not tied to tech), and more "junker" skills instead of shoving all junker effects i na single skill.
If you wasnted it to be more about colonies, it should have skills that boost the fleets of your factions, make your faction officers better, let you control your faction better (for example a skill that let you from afar call your faction for help, so the Patrol HQ fleets can be used by you in combat), etc...
Right now the industry tree feels like a big mess with tons of half-baked ideas, and considering two of its skills ended on leadership it is clear it is affecting the rest of the design too.
Also if you planned for people never wrapped around, why on earth a ton of synergistic skills are on same tier and same class? It is obvious anyone wanting more salvage will also want more cargo to carry that salvage! So if your goal was that people would stop at tier 4 you are screwed up there, because if the person wants to play as salvagar he is guaranteed to want to wrap around to have the cargo skill too, so if you put the colony skills there to keep them out of the way, you basically forced any salvager player to take a useless skill.
Neutrino Skill and Traverse Jump skill also both are great for exploration oriented players, and thus it is highly likely they would want both. So again if your idea was people would avoid wrapping around, you made the tier combinations go against that design.