Maybe it's already to late now, but I have to say I am still not quite satisfied with the phase cloak mechanic. From what I gather others feel similar. Not even necessarily because it's too weak, but because it lost all the scariness the initial concept promised. Also because it is not well distinguished from the Fortress Shield. So this is another attempt to come up with an improvement.
In the naval model, phase ships were originally envisioned as submarines – able to hide in another dimension and pop out for surprise attacks.
Full invisibility is the most disruptive aspect – managing the uncertainty of where a phase ship could be, and making guesses to counter it, is where most of the problems would come from – that has to go.
Now I read a bit about WW2 submarine warfare, and submarines could by no means be considered fully invisible. They were only hard to detect until their initial attack, after which they had to employ advanced group tactics (Wolfpack) to be successful.
I think it might be possible to transfer this initial invisibility to phase ships.
Suggestion: A ship could enter the map already cloaked - but now fully undetectable. It would produce flux like normal, so this ability has a time limit. After the ship decloaks for the first time it behaves like a normal phase ship.
It would mesh very well with this mechanic if phase ships
in a fleet were undetectable on the campaign layer.
This way the whole "management of uncertainty" aspect would be avoided. Before a phase ship decloaks its enemy doesn't know it exists, the AI
or the player could not behave any differently to handle it. You would just have to life with the possibility of a phase ship appearing without warning. Once it is revealed there is nothing different from the current mechanic.
For the lore this could be simply explained by a great amount of time it takes to "deep-phase" or by sensor adjustments to detect the specific phase ship.
This would make phase ships more interesting, more distinguished, more fearsome and allow for new tactics. For example the deploy timing of a phase ship would now be critical, and the decision for the initial decloaking would be a grave one.
Of course there are also problems with this, but I will leave it to you guys to point them out. Overall I think it would be worth it.