Interesting what you suggest to nerf it, but in that way what it still remain useful? If you remove mines you remove it main distinct feature, without that there will be no sense to use that at all. And still, all phase ships are glass cannon, I think they should be powerful because they very vulnerable to damage, and Doom only one which can effectively combat fighters and ships with Omni shields.
Nerfing is always unfun. Just take for example Supreme Commander Forged Alliance Forever - how authors of it massacred my boi Scathis... They nerfed it to ground from vanilla, by reducing its radius, which basically remove from Cybran faction game-ender unit, and nobody ever build that, then they reworked it, but still, vanilla game Scathis is better. If you nerf everything to ground again, you just remove fun stuff, it will not make gameplay more diverse, you just replace one Meta with another, with frigates which destroys everything, including capitals and doritos.
If you want really good example of good balance and diverse gameplay look at game which clearly inspired combat in StarSector, especially Flux management idea - MechWarrior series. Almost everything is useful, you can make melee mech with SRMs or array of AC-5, you can make long range sniper, or LRM boat, and everything can find it use, not unlike StarSector where some options definitely worse than other.
And weapon balance overall is also better in MW, limited ammo for example, it works in MechWarrior, but in StarSector I never use such weapons, main reason what MechWarrior doesn't have any regenerative shields, also you can add ammo as much weight allow in MW, and its better in SS spend some OP from missiles on Flux stats or even hullmod instead of using very limited weapon, and you can always make sure what you have enoght ammo for entire battle. In SS ballistic, especially large ballistics often un-effective, only Mjolnir is overall good weapon, but flux inefficient, while in MW they are really great weapons.