After playing for quite a bit, I think that the concept/idea behind the new skill system is much improved, but there are a lot of details that need to get ironed out before it plays well.
I think the most basic improvement would just be to increase the level cap a bit (maybe to 20). That would make wrapping feel much more useful and generally let the player get a few more QOL type skills without sacrificing the really good tier 5 skills. With how difficult the late game has gotten (a good thing), I don't think a small power increase from additional skills would be an issue. I do think leveling is a bit fast right now, and maybe that could be slowed down.
In terms of combat skills, I understand and agree with the desire to allow for specialization, but I feel like some of the skills are a bit too specialized. To me it makes sense that you want specialization type skills to benefit you in a way that most/a majority of ships could take advantage of to some degree, but that will benefit some specific ships a lot more. I think pure carrier skills that benefit the piloted ship only are a bad idea. Carriers are just generally not very fun/interactive to pilot. Fleet-wide carrier skills are ok in concept, but a bit weak right now. Phase specific skills are a bit too limiting in the sense that they are useless on all but 4-5 ships IMO. I prefer buffs to specific ships types like that to get added on to more general skills.
Some specific ideas to improve the current skill tree with skill rebalances and shuffling:
I think combat is pretty close to being in a solid place, most of the skills seem pretty interesting. My ideas:
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Swap C1R (strike commander) and C2R (point defense). Moderately buff the point defense skill for the piloted ship (maybe adding some of the IPDAI buffs like ignoring flares/improved target leading or improving weapon turn rate). To me strong PD buffs vs maneuverability buffs is a more interesting choice, and I could see going either way regularly.
I would also rework strike commander into a missile + bomber buffing skill instead (bonus damage and extra hitpoints for all missiles from the piloted ship and fighters basically), and nerf target analysis to be ballistic/energy weapon only. Choosing between general weapon damage, and missiles damage seems like an interesting choice to me. I would probably move the extra fighter damage from current Strike commander to be fleetwide in L3R to help it compete with other leadership skills (and make carriers a bit better). It could also be it's own skill in leadership.
For tier 3 combat, I think the tradeoff of ranged damage vs armor is good, but ranged specialization needs a small buff. Maybe something as simple as making the ranges 700-14/1500 to make it more generally applicable. Another idea is to make ranged specialization buff beams in some way (10-20% extra damage or doubled effect for beams maybe) since beams generally have long range and also feel a bit weak ATM.
For tier 4 combat, I would personally remove the phase skill (maybe try to put those buffs in other skills like helmsmanship, or in the tech tree) and possibly replace it with a general offensive skill, maybe improvements to anti-armor i.e. increase hit strength for armor penetration type stuff? I also think it would be interesting to have target analysis against shield modulation as a choice (again offense vs defense), but I'm not sure what I would put at C2L in that case. I do think the I2 skills could be moved to combat so maybe to combination of shuffling those skills into combat and moving combat skills around could work. I think a pure phase skill is too limiting in terms of the ships you can pilot, I'd rather see small benefits to phase piloting distributed through a bunch of different more general skills that you can stack if you want to be good at that. Phase ships are also pretty busted so I think a nerf is called for in some way anyway, and a phase only skill will always be on a knifes edge of overpowered and excessively niche depending on how good phase ships are.
I think C5 is good as is, systems expertise might be too good with Doom.
Leadership feels a bit off to me and I don't have as many clear ideas. Some thoughts:
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I think L1R is filler (except for some wild derelict contingent hyper cheese that will hopefully be gone soon), and pretty out of place in leadership. I think it should be replaced with something completely different or moved to industry. Maybe a bonus damage for fighters type skill to contrast the bonus damage for ships skill in L1.
I think it should be possible to take both L2 skills without wrapping, one of them should be in a different tier. Maybe swap wolf pack and carrier group so that the L3 choice is lots of PPT and damage for frigates or a little CR/PPT for everyone?. I think coordinated maneuvers vs carrier group is a more interesting choice too.
I think L4 is a solid choice.
I think L5 is strange, I really don't know what to do with it. Neither of the skills seem super enticing, but I don't have any great ideas for replacements. I don't think the raiding boost is necessary when you can just get more marines, ground defenses can be super boosted with items and the planetary shield, and stability is much less important now that it doesn't hurt income until it's below 5. The other skill is fine I guess, but it buffs income and defense fleets which can already be buffed well beyond any practical benefit without it.
I think tech is best tree at the moment in terms of power, but there are some significant balance issues IMO.
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Tier 1 is a tough choice which means it's good! It's also tier 1 so it's easy to wrap around and get both and you get both the abilities from the campaign which makes it a lot less painful. I think if the level cap got raised a little to make wrapping more viable, this would be in a great spot spot.
Tier 2 is pretty good as is IMO (assuming the confirmed change of moving +ecm to elite in gunnery implants). I almost feel like +ecm for frigates doesn't make a ton of sense though, T3L already makes frigates quite good at improving fleet ecm. I almost wonder if capping ecm range reduction at 10% (or less) might be a better elite skill for GI.
Tier 3 is a non-decision. ECM is virtually mandatory, and the carrier skill isn't even that good with 6 bays. I'm not sure how to fix that. Maybe get rid of the ECM skill?
Tier 4 is another weird choice, flux modulation is super good in almost every situation, and more importantly, it's quite good for phase ships, so it's a hard sell to take a phase ship only skill over a skill that benefits all ships including phase ships. I would rework the phase skill (similar reasoning to not liking excessively specialized combat skills). Maybe some sort of fleetwide shield/phase cloak upkeep reduction? Another idea is to make one side of T4 dissipation increase + upkeep reduction and the other side capacity increase + venting rate improvement or something like that.
I think T5 tech is in a decent place, but only if you use radiants. I would increase the automated ship point cap and also increase radiant DP so that the skill is similarly powerful, but gives you more options. I don't have that much experience with the automated ships skill though, so I'm less sure about that.
Industry is the strangest tree to me.
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I1L seems very weird. It's like 'if your fleet is small, you need less logistics ships', but logistics ships are cheap, and fleet slots are only an issue if your fleet is large where the skill doesn't do much anyway. It would have been nice for phase fleets if the new phase hauler didn't exist. It's also paired against bonus salvage and resources which is quite good. One alternative idea for I1L is to improve the chance of finding rare items.
I2 feels like it belongs in the combat tree. I almost want there to be 6 tiers in combat and 4 in industry for that reason. Alternatively, you could replace either of the the phase skills with these skills, and put some other skill like a d-mod effect reduction skill in I2. I think shields vs a repair skill could be an interesting choice in C4 (maybe with some additional ion damage resistance or something to make a t4 skill?) I guess it's a somewhat interesting choice though, with both options being good on a decent subset of ships, and useful on any ship. Not a bad pair of skills, they just feel out of place in industry IMO.
I3 is a solid choice IMO.
I4 has derelict contingent, which is busted/needs a total rework, and field repairs, which is the 'I hate d-mods on principle' skill. Replacing DC with a skill that reduces the impact of d-mods would be more thematic IMO. I think I like field repairs in its current state though.
I5 are both good colony skills that will make lots of money, but making lots of money is meaningless right now. We will have to see where late game goes before really judging these IMO.
The more drastic suggestion I have is to abandon the restrictions of 5 tiers and 2 skills per tier. I think you could improve the trees a lot by adding third options in places. Also not having to worry about having enough skills to get get 5 tiers, or having to cut skills to get down to 5 tiers would be a benefit IMO. Effects like the old bonus damage/armor for armor calculations skills seem to have been completely cut, and there are also several skills that feel like filler right now where I would almost not mind some rearranging/combining to lose a tier of skills. There are also skills I would move to a different tree without the tree structure restrictions.
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