I'll give this a shot
Combat, Tier 1
Helmsmanship is something I view as more-or-less necessary, with the only possible exception being carriers, so having a choice between those two seems good. This breaks down if you want to loop through the tree to get more of it's stuff. This probably won't be the case for all but the tier 2. Armor vs Range and Shield vs Cloak are generally things you don't want both of. A Gryphon pilot would want both tier 5s, but would probably be fine with just missile specialization.
Combat, Tier 2
+20% Damage to Capital Ships and +100% Damage to Weapons/Engines are both huge buffs that I can scarcely imagine passing up. Sure, I want to kill missiles and especially fighters, but at that opportunity cost? And they're less dangerous in this version of the game. I guess I could see it for carriers, again, but they wouldn't get much benefit either. This is one where you might want to loop through to pick up, except that would require spending 1 of your 15 points on Strike Commander.
And here I'll bring up a concern: If I looked at this skill screen and said "I want to be a carrier captain (or commander)"... I wouldn't be able to do that. There's a grand total of one personal carrier skill and one fleet carrier skill. And the fleet carrier skill is like +3 fighter bays' worth of replacement, always, and if you have a carrier in your fleet that you're not bringing into battle or just making great use of, then screw you, that's coming out of your paycheck. Yeah, they were too strong before, but this can't be good design.
Combat, Tier 3
A 1000 range weapon on a capital ship reaches the 1600 mark, and if you can dictate the range of your engagement, then you can make full use of this bonus. However, anything that can reach this range cannot dictate the range of their engagement, and are almost certainly fighting enemies that will get much closer, and are likely to crawl closer under AI control unless you meet some serious restrictions on loadout and/or officer. Alternatively, big happy armor. Impact Mitigation is a lot more valuable than it may first appear. My first campaign I ignored it. I have shields, I'm in a light, fast craft, who needs it? But even then, the Impact of this skill can be huge, saving a lot of pain when shields can't stay up or if you're just a bit incautious.
If Ranged Specialization was based on the maximum range of the weapon rather than the distance of the engagement it could maybe be worth taking for some ships.
I also don't like that the +Projectile Speed effect is attached to this particular skill. My Apogee Plasma Cannons really want that boost and they're not gonna hit at those ranges.
Combat, Tier 4
Simple, straightforward, are you driving a shield ship or a phase ship? Or are you a madlad in a shield-override ship, in which case screw you?
Combat, Tier 5
Hoo boy, these are ship-dependent. Missile ships tend to have either autoforges or fast missile racks, and Missile Specialization is both on one, where Systems Expertise is one or the other. Systems Expertise does a lot for some ships (most triumphant example being the Doom) and nothing for others (Paragon). As this is the last tier, there's no pressure to take one if your ship can't benefit from it, though on the flip side it's disappointing to reach the end of this progression and just skip on the final step.
What I really don't like about this one is that if you can't benefit from the general skill, you can't benefit from the specialist skill either. The ships that don't have systems that synergize with Systems Expertise are not missile ships.
Final thought: If there were three options per level, one level could be armor vs shields vs phase and another level could be systems vs point-defense vs missiles or something.
Leadership, Tier 1
The recovery cost limitations are so low that you can't make much use of these. As much as I like the idea of bigger bonuses with smaller fleets, it doesn't really work well when you need reserve forces, nor does it work well with how things scale up over time. And since it's recovery cost and not deployment points, it further encourages you to keep less-impactful d-mods on your ships, rather than trying to get a pristine fleet, which I don't like. There was already some of this encourage for keeping your costs down, and I let that slide because I like to keep my costs down, but this is starting to get annoying.
If it scaled with player level (so Auxiliary Support was, say 1*level instead of 5), or was dependent on the size of your deployed fleet, it would be better. As it is, it is rather at odds with the game's design. You're supposed to be building up to bigger fleets to take bigger challenges, and if that just lowered the bonus, then fine, but it currently gets lowered into obsolescence and that's not fine.
As for these particular skills - +10% fleet damage would be great if it was actually that (and maybe too strong for a fleet of any size), Assault Package with the buff could be relevant for a Venture, and an Escort Package Phaeton or something could be okay... maybe. I don't like that militarizing my ships for burn and sensors pulls from this bonus.
Leadership, Tier 2
With the overabundance of enemy officers, you will quite regularly encounter fleets with full nav and ecm, so countering that is a serious concern. What was easy to spec into before is now... not. And as much as I'd like to have 3 frigates hanging around giving me the full +20% nav, that ties up three officers and is mutually-exclusive with the +120 seconds operating time that would actually keep them on the field. And I could loop around for both, which would require going through the horrible, awful, no-good tier before it AGAIN.
Wolfpack tactics is kind of neat though. 3 Tempests with officers have been handy, though I haven't quite figured out how to keep them on the field for an entire battle yet. Maybe if I gave them both Helmsmanship and Auxiliary Thrusters they could dodge everything.
Frigate-exclusive command point recovery is just weird. Why is that a thing?
Leadership, Tier 3
Combat Readiness is really great. Fleet-wide combat readiness is really great. The limit on this one is high enough that it doesn't fall into worthlessness even endgame... barely. Still not good.
Fighter replacement as the one bonus on an entire skill could maybe be good enough in a big carrier fleet... but it diminishes with number of fighter bays. Yeah, nah. Again, if I say "I want to be a carrier commander"... there isn't really a skill for that. And if I'm not saying "I want to be a carrier commander", why would I even look at this thing?
Leadership, Tier 4
Originally I thought +levels to 8 officers would just be better than +2 officers. In exploring around the sector, I've picked up a couple Steady level 7s though, which I suppose I'll keep, and a few level 6s as well. So it's, what +levels to 4 officers, instead? And I've still got more of the sector to explore.
What I don't like about this choice is that I can't really analyze it. How can I know which one will be more valuable to me? I don't think I can. If I look at Combat Tier 4, I can say "If I'm gonna drive a phase ship, then the phase ship skill is more valuable to me", but I can't think of any parameters I can set under which I can analyze the comparative value of these skills.
Leadership, Tier 5
There are four colony skills in this game. If I say "I want to be the best colony manager", I can spend my 15 maximum skill points to pick up 3 of these 4. Not that I would, because I like to play for the long game, and in the long game I have alpha cores to do that for me. Though I suppose, in this version, I can respec when I don't need them anymore.
Aaanyway... I don't really care. If I want to get serious about having a big bad ground force I'll take Ground Operations. If I want more money I'll beef up my combat skills and whack some bounties. If I want to defend my colonies I'll build up some defenses and in the worst case, I'll bring my fleet. I'm not feeling these skills.
Industry, Tier 1
With the limit in place, Bulk Transport's capacity bonuses are less about having a more effective merchant fleet and more about doing away with a few logistical ships altogether - like having an Atlas and half a Prometheus without actually having them. The burn bonus would be great with Auxiliary Support so you're not militarizing ships to get them up to speed and taking away from the actually-militarized ships' bonuses... except I still want the sensor bonuses.
Salvaging is handy for extending exploration forays and picking up more weapon salvage... probably doesn't give more AI cores. Might be something to stick a point in early game and then respec out of when you've kitted out your fleet.
Neither of these bonuses are very good, and I wouldn't like to be stuck with them all game, but I guess that's no longer a concern, so...?
Industry, Tier 2
Damage Control mostly reduces the hurt when you screw up, and I'd much rather prevent damage than reduce it. However, I believe the faster repairs applies to EMP damage, which is really handy. However, it's competing with +15% readiness and +60 operating time, which is yes, so no. And Damage Control isn't good enough to circle back for.
Industry, Tier 3
If I said to myself "I want to lower my fleet's operating costs", this is the tier where I'd make that happen. There are two skills for that here, and I'd get one of them. If I said to myself "I care about doing literally anything else", I wouldn't care about either of these skills. So I think this is a bad tier, these shouldn't be competing. There just isn't enough difference between lowering fuel costs and lowering supply costs. I like them both, I want them both... and if I didn't want one them, I can't imagine a situation where I'd still want the other. And that's one thing, and another thing is wanting to spend precious skills points going through the previous tiers to get them.
Industry, Tier 4
Field Repairs. I remember having this skill in my previous campaign, and I miss those days of instantly-removed damage and fast repairs. But that maximum! In my current fleet, I'm looking at +18% and 9%. That's just not good enough. Maybe if I had a heavily d-modded fleet to bring my deployment recovery cost down... oh look, this skill also passively removes d-mods. What.
I'm not going to comment on Derelict Contingent. The idea of actively pursuing a heavily-d-modded fleet is vaguely interesting, but I'm ultimately uninterested in trying to analyze this.
Industry, Tier 5
If I want one of them, I want both of them, which would require 2/3rds of my skill points to achieve. If I don't want one of them, do I really want the other? ...Well, maybe. An affective +2 colonies can be handy for multiple things. And It's something I would consider taking on my current run if I didn't have to go through the rest of Industry to get there.
Final Thoughts: I want to like this skill system, but as things stand I don't. I think 3 options per tier, 4 tiers, could work a little better, depending on what the new skills are and how it's all organized. I think it's a mistake to put all the colony skills at the end, mutually-exclusive, rather than letting the player spec into them.
...And I just realized that I completely skipped Technology. How did that happen? Well, this is already long, maybe I'll post something on that later. Short version: Special Modifications is the strongest skill in the game, Automated Ships is a weak novelty, skill maximums continue to be annoying in how they're implemented, the first two skills are really great and you can just take both after getting to Special Modifications, Gunnery Implants and Energy Weapon Mastery are both great, especially for Frigates and Electronic Warfare is more-or-less necessary for keeping your range, I completely forgot that Fighter Uplink exists, Flux Regulation is also good, even with the limit, Phase Corps would be nice without the limit and if it wasn't competing with the really good stuff.
Edit: I just realized that there's another part to why the game feels harder than it used to. The AI's masses of frigate officers gives them nav that I no longer have and more ECM than I'm used to. Full nav and ECM (and other speed/range bonuses) is how I chumped the Blade Breakers. It's a big deal.
Three Tempests with Gunnery Implant officers and built-in Nav Relays may be astronomically valuable. If they can stay alive.
