Currently, energy mastery is only useful for small ships with small hard-flux energy weapons.
Well that's just factually wrong. Energy mastery is useful for bringing energy PD systems up to par with ballistic PD systems. As it stands, energy PD has longer range than ballistic but lower damage, but energy mastery scales up that damage so that tough or numberous targets can still get popped quickly before hitting the ship. And of course, the elite version of the skill is enormously useful for any ship with a heavy energy loadout, high tech or midline. It's great for Paragons, Auroras, Champions, and fantastic for PD Medusa setups.
I suppose this is in addition to Point Defense. If boosting energy PD is priority, then taking Point Defense before Energy Mastery would be a better idea. More damage (and more range if elite). But energy PD would indeed be boosted by Energy Mastery provided the ship has significant flux, so your point stands on that case.
The elite part of Energy Mastery is the only good part of the skill, which I can only rely on my commander and AI cores I use. If my officers can only have one elite skill, I probably would not use it on Energy Mastery.
Range is indeed very powerful, and the AI being scared for no good reason is a large contributor to that (although SIM Falcon is a bad example because its speed and weapons are the perfect soft counter to High Tech). But at least on paper non-Frigate ships with good speed should prefer other skills, unless they are specifically built for kiting with 1000 range weapons. Target Analysis, Energy Weapon Mastery, Field Modulation, Helmsmanship, Systems Expertise, Missile Specialization, and of course Ordnance Expertise. Edit: or the powerful Elite Point Defense + small mount weapons combo
Or what about missile boats and carriers? Ships like Gryphon and Heron don't need gun range, but using Ordnance Expertise on them saves a ton of OP on vents.
Or SO ships? Aside from the obvious Frigates for which 4% ECM is worthwhile?
Falcon is fairly common in endgame bounty fleets, and ships get separated at times and end up in duels, so the "bad example" SIM Falcon is not too contrived.
As for Gryphon, it most certainly can use gun range. It can use enough guns to brawl like a destroyer or Falcon, which is handy if I do not use Squalls on it.
For carriers, that varies by ship, loadout, and AI behavior. If it has guns and not using expensive bombers (and AI is aggressive enough), then carriers too can especially use the gun range.
For SO ships, okay, range boosters (and weapon accuracy) are downplayed.
About Industry tree - actually the fact that Ordnance Expertise is locked behind a non-combat skill is the reason I don't get it for my flagship. Because I want Automated Ships, Best of the Best and either Systems Expertise or Missile Specialization. (I do start the game with Industry 5, but then respec out of it after my colonies start giving me infinite money)
I generally want Hull Restoration, Automated Ships, and at least three combat skills for more mobility and PPT/CR.
I get Industry primarily for Hull Restoration. It makes casualties much easier to stomach. Plus, it is the only cheap way of repairing ships the player cannot build or buy, like Ziggurat or any automated ship. Automated Ships is fun at times, although I have considered dropping it and some other Tech prereqs for Leadership (or other) skills.
I would like Best of the Best, except if I reassign skills after getting a third s-mod, I lose them all without any refund, and that really hurts. However, the best thing about BotB is removing unwanted s-mods on exotic ships by getting three s-mods then selecting the one s-mod the player does not want after removing BotB.
I like to get at least five Combat skills, but I do not take System Expertise or Missile Specialization unless the flagship I want really needs the skill to become much stronger, like Systems Expertise on Doom or Radiant. For Combat, I always take Helmsmanship and Impact Mitigation for mobility (and armor for armor tanks) and Combat Endurance for more PPT and slower decay if I want to pilot a small ship or SO ship. After that it varies. If I pilot a Paragon or phase ship, I want Field Modulation. If I pilot something that wants to use HMGs or various midline and high-tech ships that can mix railguns or needlers with beams, Ballistic Mastery. If I want to rely on small weapons for offense, Point Defense (for the elite effect).