What skills the player should be most interested in if he looks down the line and wants the best for endgame play.
Combat is where things are at. Players probably want to be at least as powerful as a level 20 officer. Detailed skill analysis has been done elsewhere and not really the point of this topic, and nearly all have their niche or use, except Helmsmanship 3. Helmsmanship 3 is useless because moving at zero-flux speed with shields up only works when there is no combat and no need for shields.
Leadership has some useful skills or necessities. Command and Control enables an unconventional playstyle. Officer Management is one of the most powerful combat skills if you can deploy your whole fleet somehow. Fleet Logistics does several very useful things even if the colony bonuses are ignored. Coordinated Maneuvers removes the need to capture Nav points. Carrier skills are combat skills for fighters. Odd one out is Planetary Operations, which while good, is mostly colony stuff that is free with an alpha core. Raiding bonuses are nice, but unnecessary for stealing blueprints - just get more marines. Your character may not want everything here, but some, like Officer Managment and Fleet Logistics, are among the best for everyone. The only one that is really unnecessary is Planetary Operations is because while useful, you can get the colony benefits for free with alpha cores.
Technology is a mix of powerful combat or other vital skills whose usefulness has been explained elsewhere. Sensors is the weakest link, but even that skill has some use.
Industry skills seem mostly those that deal with problems that go away by endgame. Safety Procedures is the only one that seems endgame worthy if one wants to E-Burn frequently or exploit lowered malfuction thresholds. The rest of its bonuses apply to crew and clunkers. Crew, you can easily buy more than you need, and for clunkers, you do not need them at endgame when you can afford and build as many pristine ships as you want. Recovery Operations, the only perk that could be useful late is the one less (D) mod that sometimes lets your pristine ships that were disabled stay pristine when recovered. Field Repairs is convenient, but nothing that more money cannot solve. You do not need Salvaging by endgame after you have found every blueprint in the game. It might help find more special items, but the skill is usually not needed, and raiding core worlds for the item is a last resort. Colony Management and Industrial Planning are very useful, except it is better to abuse more and more AI cores that can be farmed and have Industrial Planning and other skills, than get the skills yourself.
In short, skills or perks to avoid when seeking maximum endgame power, and why:
- Helmsmanship 3. The perk is simply useless.
- Colony skills aside from Fleet Logistics. Free from alpha cores, cores are safe to use (thanks Pather bug), and theoretically unlimited cores may be farmed by those who can smash Ordos fleets.
- Other Industry skills. Their perks become progressively less useful as player acquires more income and loot, then be able to easily afford and casually replace anything lost by endgame.