Everything in the game is fair and counterable, except phase ship abilities.
Absolutely no response exists to them, targets simply have to accept the consequences.
Amplified Entropy is a significant, long-lasting debuff. No way to stop it.
Quantum Disruptor is a severe, short-lasting debuff. Once again, no way to stop it, and used right it can do immense damage effortlessly.
Mine Strike is like being able to instantly land a torpedo or five on any target that is not shielding its trajectory, i.e. anything protecting itself while retreating. Neither players nor AIs can possibly hope to respond in time, and it's by far the most overpowered ability in the game. My complaints about Mine Strike extend to Star Fortresses.
Amplified Entropy just isn't a fun ability to play with or against, even if it gets a rework. Something else would be better.
Quantum Disruptor would be pretty neat as a slow electric pulse. Still unavoidable for large ships, but the issue with it is really that it can instakill small ships. When modding another game, I found that the ideal way to render a slow electric pulse is not to have visible things move but instead have a moving wave in which stationary (though still animated) sparks appear.
Mine Strike should have an arming time that gives ships and fighters a few seconds to respond.