All of the Combat skills, except for two, are tier 1. Does that mean that they either are or should be worse for combat than tier 2 skills in other trees? While in many games, skill tiers tend to denote clear demarcations in power, that's not really how Starsector works, considering that capstone skills are available during the early game by level 5. Even you seem to realize how the skills seem to have been slotted all wrong based on their combat power. Have you considered that maybe that's a feature and not a bug?
It may not have been intended for tier 2 combat skills to be necessarily more powerful than those in Combat, but Ordnance Expert and Gunnery Implants at least turned out to be noticeably stronger than them. Energy Mastery is mostly for close-ranged specialists (lame for large ships that fight near or past the 1000 su range), and Polarized Armor is vital for those without shields but nothing spectacular for most others.
Tier 1 = Most Combat and Leadership skills, some Tech and Industry campaign skills.
Tier 2 = Tech and Industry combat skills.
Tier 3 = Tech fleet (combat) skills, Industry campaign (non-combat) skills.
Tier 4 = Leadership officer skills (and for human officers only, Combat capstones)
Tier 5 = Capstones
(I sometimes forget that tier 3 Leadership is actually tier 4 because the Officer Training/Management skills have three skill prereqs like officers' combat capstones, while Tech and Industry skills between tier 2 and capstones only have two prereqs.)
I have little to no problem with the Combat tree aside from officers needing fewer levels than the player to get the Combat capstones. Officers can easily get both capstones while player needs to spend too many skill points to do so. (Looks like a favor for those who prefer armchair combat.)
I do not have any problem with Leadership other than envying how strong it is as a whole. I think it is the most powerful tree in the game.
I have no problem with Tech up to tier 2. After that, Technology seems okay in theory (fleet skills offering fleet combat power like Leadership), but I have gripes with some skills, and I think the capstones are underwhelming despite unlocking weird fun stuff, which I wrote about before.
I have no problem with Industry up to tier 2, but after that getting the campaign QoL is not worth sacrificing the combat power (aside from possibly Derelict Ops.), even if the QoL is fun or mitigates campaign annoyances.
I think capstones should be worth more than one low-tier combat skill worth of power.
(Not sure if all that answers your question satisfactorily.)
This is true, but by the point that a 100 CR baseline fleet has given up all of its bonuses, it can still fight with an expectation of victory 2 more times without any recovery time. A fleet running primarily on the baseline CR would begin with 40% CR. How's that fight going to go?
100% CR means Hull Restoration
and BotB (otherwise, it would be 95% CR) and either Crew Training or Combat Endurance. A similar fleet without Hull Restoration would be 85% CR, not quite baseline. If fleet has both Crew Training and Combat Endurance on all of the important ships, it would be 100% CR anyway for the ships with Combat Endurance.
But the difference of 10 to 15% is basically one fight, provided the ship is not too damaged for another round after fighting. The two ships that need to rely on stacking CR are Ziggurat and Radiant with a Beta+ core. Ziggurat needs more than 90% to fight two battles in a row, and Radiant with Alpha core starts with 20% CR (though practically 35% since Combat Endurance is a given) and needs at least one more source of CR beyond Combat Endurance to go above yellow.