I don't think raising the level cap fixes the issue. It just results in you taking more fleet wide combat skills IMO. I think it's fair to argue that splitting combat skills off would eliminate some possibilities (taking no combat skills), and there are probably better approaches. I guess my favorite idea is making skills cost different numbers of skill points as way to balance them without having to gut the strong skills, or try to make all skills equally strong.
I think it's coming down to play style differences, different evaluations of skills, and different fleet compositions.
Generally I grab 5 skills in the combat tree, simply because on the right ships I consider System Mastery to be a literal game changer on the right ships, and Missile Specialization isn't that far behind (although the later can be partially duplicated by having an Combat Endurance/Missile Spec officer sit in the ship and swapping at the start of combat, which also frees up a combat endurance pick on player character). So in some play throughs, I nominally trade 5 (or 6) officer skills for 2 half skills on my personally piloted ship. On the other hand, I might only have 8 combat ships filling out 240 DP in such a run, at which point am I really trading anything away if ships are actually DP balanced?
From my experience in vanilla, you can be successful with the no personal skill style as well as the 13 player skill style, or anything in between, assuming you have an appropriately designed fleet for the skills you chose.
Success is a super poorly defined term.
I define success in Starsector as the ability to use a 240 DP fleet (on a 400 DP default combat size setting, since on smaller settings personal skills become more valuable relatively speaking) to defeat a pair of [Super Redacted] at a Hypershunt, a single triple Radiant Ordo after farming a red system for awhile, and take out the [Super Redacted] bounty, with the outcome never being in doubt (3 out of 3 replays result in victory). In addition, being able to get to that point in the game on iron man with a spacer start without taking a commission or respecing, and in a short enough time frame I don't lose interest in the run. Others may have different definitions of course, but I feel like that one covers most of the bases in terms of end game content.
I agree the direction that balance moves you in is important, but the problem is you have different players with different styles at which point different skills are going to pull on players differently. I highly value personal ship skills, but then again, my default or typical combat play style is issue a few move orders at the beginning, engage the enemy, and cancel all my orders, and rely on my support ships to survive and essentially be distractions, while I fly around picking enemies off. I'll sometimes pop up to the tactical map, or if I'm not in an end game fleet and I feel the battle is close I'll actually issue further orders (harass a capital, eliminate that flanking ship, etc). I guess what I'm trying to say is what appears strongest to a player is going to depend on how they actually approach the game.
RE 'my good fleet can't use these strong fleet-wide skills'
From the perspective of pure optimization, the response would be that the fleet is probably worse than another fleet that can use those skills, and you should just use different ships (for instance just remove some capital ships and add more hyperions to use the extra officers). You can of course do many things that will work, but I am trying to talk about what the game is incentivizing you to do, which is the 'strongest' thing.
I’m very good at combat but when comparing the benefits of adding Support Doctrine (with my 10 unofficered ships) vs. Ballistic Mastery for my flagship, the impact of the former is magnitudes higher than the latter. And this a real choice the game gives you. All Tier 0 Combat Skills ultimately compete with T3/T4/T5 skills for your skill points
It's easy enough to say in general and in vacuum, but you really need to have a concrete example, since there's always tradeoffs. For me my end tier leadership skills are competing with Missile Specialization and System Expertise, not the tier 0s.
So for example, your optimization choice for my proposed fleet is unclear to me. Swapping, say an Onslaught and Fury for more Hyperions to get more benefit of 2 more officers comes at some cost. It's another 9-12 story points to s-mod the Hyperions and mentor/elite skills the officers for example, on top of the already spent 58 (8 for mentoring, 2 elite skills per officer, 3 s-mods per ship times 9 ships, 7 personal elite skills). The former requires 2 story point past level 15. The later requires 15. If story points are no object, and we're doing pure optimization why would you ever take the +2 officers skill when you can just hire two mercenary officers?
So to make it concrete, lets assume I'm piloting an Onslaught XIV, my baseline fleet is 2 Onslaught XIV, 2 Legion XIV, 1 Fury, 4 Hyperions, and my skill selection is:
Combat Endurance, Impact Mitigation, Target Analysis, Ballistic Mastery, Missile Specialization
Wolfpack Tactics, Crew Training, Carrier Group, Officer Training, Best of the Best
Navigation, Gunnery Implants, Flux Regulation
Field Repairs, Ordinance Expertise
Dropping Missile Specialization defeats the point of piloting the Onslaught since the plan is to drive up flux at long range with 4x Squalls and 8x Longbows from escorting Legions, and Thermal Pulse Cannons at 1950 range, and then burn drive in and drop 4 Reapers at point blank (and a 2nd salvo if necessary 10 seconds later within the overload duration, such as against Radiants). 5 other smaller ships tends to be enough to keep the rest of the enemy fleet distracted while I quickly focus fire down capitals and cruisers.
I suppose you could drop the Field Repairs and Ordinance Expertise, but it's not clear to me the two extra Hyperions are really that much better than an Onslaught in such a fleet, and the loss of flux on the player ship is quite noticeable. The extra capital provide some nice staying power in long slogs (like against multiple large pirate fleets or the like which just take time to churn through all the hullpoints) that the Hyperions lack.
So assuming the player wants to use a shiny Onslaught XIV, and found 2 Legion XIV (like I did in my last play through - it admittedly doesn't always happen), how would you respec the character and rebuild the fleet with minimal player skills and 11-15 fleet skills, while keeping that 3 ship low tech core, working under the assumption that fleet skills are going to be superior generally? That'll let me try flying around both setups and at least I'll have a personal testing experience against a hypershunt and Ordos I can relay back.