Wait, you think the skill changes between .95 initial release and now were that drastic and BAD for non-phase ships?
Skills:
Gunnery Implants:
Switched elite effect (-50% recoil) with the electronic-warfare-boosting effect
Pure buff for ballistic ships and stops non-Remnant fleets from destroying the player with ECM. Significantly lowers the value of Gunnery implants on frigates like phase ships.
Now also applies a 1% ECM bonus on cruisers and capital ships
Electronic Warfare/ECM: reduced maximum range reduction to 10% (was: 20%)
Coordinated Maneuvers: now also applies a 1% nav rating bonus on cruisers and capital ships
More buffs for non phase frigates. ECCM to 10% is a major reduction in remnant fleet power.
Energy Weapon Mastery: reduced max bonus damage to 30% (was: 50%)
Nerf to phase ships and high tech ships, including endgame threats, makes this an indirect buff to everything else.
Impact Mitigation:
Changed effective armor bonus to 50 (was: 150)
This is now the elite effect
Old elite effect (-50% kinetic damage taken by armor) removed
This may be overnerfed but its still an ok skill for ships with high armor. It is a much weaker skill for high tech ships and other ships with light hulls like phase ships and remnants. With how many officers enemies have, the enemy got easier to kill, which buffs all player ship builds offense at the expense of defense. Given that phase ships generally avoid damage rather than tank in the first place, this narrows their margin of error but doesn't impact their 'ideal' use case on defense.
Increased deployment point and fighter bay thresholds for some of the fleetwide skills
More skill adjustments etc will be forthcoming, but are not hotfix material
Buffs to larger fleets and buffs to carrier counts. Again, more buffs for non phase fleets.
Lets see, the helmsmanship elite perk also got removed from overloading ships, which makes it easier to kill enemies that overload on both sides. I would say thats just an increase in lethality across the board, no real change of relative compositions. If anything I'd say its a buff to non-phase ships: phase usually kills with sudden alpha bursts of AM blasters, phase lances/blaster, or mines rather than sustained gunfire on overloaded targets.
So... what were the skill changes I missed? I looked through the patch notes for changes and these are the only ones I can find, and they don't really seem to benefit phase ships that much if at all. Are you talking about built in SO getting removed, because thats not part of the skill system, its part of ship building.