As for Doom mining fighters, since fighters are effectively missiles and vice-versa, I have no problems with mines spawning directly on top of them for the instant kill. As far as I am concerned, mines are effectively anti-missile for that use.
I think the whole mindset of "fighters = missiles" is heavily oversimplifying that aspect of the game, but regardless, I hold that Doom, or any ship for that matter, should
not be a direct hard counter to all carriers like it is now.
Non-hybrid carriers nearly completely rely on their fighters for firepower, and mine spam shuts it down at pretty much zero cost to Doom, rendering the carriers useless (especially at 30% replacement rate). Notice that there isn't any other interaction like that between ships within the entire game. Imagine if there was something that could easily and permanently shut down
warships and their weapons.
Maybe the closest things currently in existence to that are the Harbinger (which can turn off a warship, but only for
a fraction of a second), Ziggy (which is a unique end-game ship, and comes with its own host of issues), and Shade/Omen with their ion emitter (which gets stopped by shield and isn't permanent anyway).
Furthermore, besides carriers, there are no other ships so heavily affected by perfect PD (except maybe the gimmick ship Gryphon, which is still a fully capable warship with multiple ballistic mounts at the front).
The current situation is simple and totally binary. If I see carriers in enemy fleet: field my Doom and never worry about any bombers in the entire fight. If I see Doom in the enemy fleet: DO NOT field any of my carriers - they'll get shut down easily.
Doom represents a nearly perfect, nearly zero cost PD, therefore it's overpowered.
Changing from fighters-as-ships to fighters-as-missiles has caused worse problems than those it fixed.
I disagree. Before the fighters-as-weapons change, there was practically zero point to piloting carriers, which were nothing but anemic watered-down warships acting as a repair point for drones which you don't even have any direct control over. I can say with 100% certainty that back then I never even bothered with carriers or fighters. They were just boring.
IIRC according to one of Alex's old blog posts, the change was supposed to give player a fun interaction with fighters and incentivize piloting carriers, which in my opinion it achieved without a doubt. I can't argue with you that the solution isn't without issues, but there is no legitimate reason to claim that it is worse than the previous system, which frankly was just horrible.