Really? The combat tree has a lot of fantastic skills, but, to be honest, they don't really 'pop' out as useful until you get into the very nitty-gritty of how combat works, and truth be told, Combat is mostly centered around the piloted ship so it's a straight investment in multiplying player skill. Basically you get to be the instrument of what you want to happen on the battlefield, specific ships destroyed early or holding the bulwark somewhere. If you play as a huge fleet with dozens of ships with you piloting one of them you don't get as much benefit from the tree, sure. Let me give you my rundown:
Ordenance expert is the simplest one to grasp with the L3 15% weapon damage boost, but the most important step there is the projectile speed, since it works in tandem with the Gunnery Implants L2 100% Autofire accuracy. Against fighters and frigates this is golden.
Target Analysis handles a lot of the more end-game issues. 15% more shield damage is very useful when you're trying to break Paragons or other shield-heavy ships (and stations), especially with high level officers in them. But the 50% hit strenght for armor damage is huge when also facing bricktanked ships like the Onslaught.
Evasive action is a half and half, but i haven't seen a ship that doesn't benefit from maneuvrability, but the L2/L3 perks are vital if you're going for anything midline/lowtech. A lot goes behind the 'armor calculation', but it's vital to minimise a lot of the smaller hits that you get, and this helps in that.
Impact mitigation goes hand in hand with Evasive action, again, vital mostly if you only go low/midline, but even so, it can help mitigate a weakspot opening up on your armor (also does magic on smaller ships, the 150 extra armor).
Defensive systems is a must, no matter what you end up playing, especially with the L3 hardflux venting passively. The boost in survivability is huge even if you only use the shields to take torpedo/missile hits.
Advanced countermeasures work with optimizing your defences against the opposite effect and while not something you want to take early, in the lategame when you want to eek out survivability while in the midst of the entire enemy fleet, this is a must.
Damage Control is.. take it or leave it. It helps to smoothen out some of the bad situations in combat, but you shouldn't really be getting in them in the first place. And the L1/L2 bonuses can be supressed with campaign logistics/credits (supplies/crew).
Combat endurance is only really worth it for that 15% CR boost for piloted ship (which translates into sizable bonuses to combat). I'd rather get Fleet Logistics imho but if i have to choose the last skill in the game, Combat Endurance isn't horrible.
Missile spec is really specific and you either take it or not, not much to say here. (Though the L1 at least is worth it since it translates into much more hits on homing missiles)
Helsmanship is eh, take it or leave it mostly, especially with the nerfed 1% flux for top speed. When it was 5% you could take some light machine guns from fighters, with hard flux dissipation, on a raised shield and not worry about it messing up your charge, but now it's really just there to be able to hold a shield up while charging. If you take this for the escape situation, Coordinated Maneuvoers in Leadership is better, but if you take this for chasing someone down, you don't want a hit to get you out of the flux-speed bonus, so you'll be flying shields-off, weapons turned off anyway, so you can unload more from a smaller gap. Overall, helsmanship ehh, the acceleration bonus may only really help with the extremes, ultrafast frigates or ultraslow caps.
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However, maxing out the Combat tree comes at the expense of fleet-level issues. You won't have enough skill points at level 50 to juggle into all 4 branches effectively, so given Technology is the second 'must' after combat (Gunnery Implants, Loadout Design, Power Grid Modulation), you either go with more 'peak' performance with Fleet Logistics/Officer Management, or better critical situation management with Field Repairs/Safety Procedures to handle multiple engagements in a row or taking riskier environmental-backed fights on the overmap.
And yes, all of this does prevent you from taking all the overmap/campaign related skills, like colony government or salvage bonuses, which will cut you off from some more exotic late-game materials. But in the end, it's still done to contextualise combat, which is where we return to actually being really effective in it.
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And since the thread talks about skills in general, i touched on a fair bit of them already, but as related to progression, the first 25 levels fly by relatively quickly so your 'core' should be set up by then. For me that's the Combat/Technology mix. If you fly carriers, it'll be the Leadership/Technology mix. If you do a lot of necrophaging with salvaging and autofitting ships with whatever and throwing them in the grinder, it's gonna be Leadership/Industry. Either way, the last 20 or so levels should be about smoothing the edges of your character and rounding it up.
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As a final note, i'm not super sure on the breakdown of the new colony skills. You have Planetary Operations in leadership, which can be considered /really/ good with the +2 stability at the end which is the only skill of its type in Leadership, and Colony management in Industry which is made to go hand in hand with that. I would have liked it to be split like "skills that intensely benefit a small handful of colonies versus skills that allow more colonies at a lower 'intensity'", but either way, either split half and half between Leadership/Industry or just slammed all in Industry.
I'm really wondering at this point whether it's smarter to have two types of skillpoints given per level up, Combat and 'Civilian' skillpoints, so you make sure the character works up without severly ignoring one entire way of experiencing the game.