I want to make it clear (just in case): i m OK with Doom, or other phase ship be OP in player's hands. What i dont like is the general phase mechanics and how we CAN interact with it (hint: not so well).
In games like starcraft we have multiple layers: ground forces, flying units, invisible units, etc.. We need specific ways to interact on different layers. And it works well. But! It works well, because all those games are about how good and fast you can adapt. Starsector is not about that.
Yes, you can go and refit entire fleet to deal with phase ships (you cant carry those specific answers against them every time because of skill bonuses depending on your fleet size), but come on! I d better skip this fight then change my course.
I like the idea of increased cloak cooldown. In any form. It must not be very big time, like 10 seconds, but, as i said earlier, we can try to start with 3/3/4/5 depending on hull size (and keep -50% from skill). Crippling phase coils sounds good, but i m afraid it might be too much. Maybe we can simply cut flux stats a bit.
AND AGAIN: reasonable cooldown for Doom's mines and for Quantum disruptor. Or how about that: add soft cooldown. If ability used before the end of soft cd, it costs more flux.