Simple suggestion to change up the combat dynamics of phase-ships.
The "issue" (matter of opinion) it'd solve how ruthless they are - The window in which opposing ships have to engage them (while at PPT and not in too deep) before they slip away is very short - they evade a hell of a lot of all return-fire, and make a joke out of range-management, making them extremely effective kiters. I'd like to be able to build ships with loadouts to effectively counter them - and for there to be more threats for players to account for when using them - and figured EMP would be an effective countermeasure that's already in the game.
There's a couple of ways this could work.
In both cases, the EMP projectile doesn't "hit", but passes through the ship while it's phase-cloaked, doing no physical damage.
#1 is projectiles/beams deal diminished EMP damage across all the parts of the ship they intersect - Electromagnetic buggery is transphasic - ships equipped with EMP weapons will have more success in catching phase-ships. Would make Automated Repair Unit, Resistant Flux Conduits more valuable on phase ships
#2 is EMP fire builds flux on the phase-ship while it's cloaked (Compensating for EM interference in their phase thingy), basically the same relationship between EMP vs. phase-cloak as kinetics vs. shields, enabling EMP-equipped ships to more easily flush them out or keep them at-bay.
These dynamics could be built into dedicated weapons of their own and/or combined within one, alternatively or in addition to imbuing EMP weapons with these effects vs. Phase-cloaked ships.