For quite some time, I've been pretty dis-satisfied with the Phase mechanics, because while they are a form of "shield", they're a shield that:
1. Does not allow DPS to be produced.
2. Does not provide any protection when producing DPS, so a Phased ship, upon emergence, may just get crippled and be useless.
3. Is totally dependent on good alpha strikes.
In player hands, the Phase Cloak ships are OK-ish; some players like them a lot. I'm not going to argue that they're useless; rather that they're pretty useless vs. upgraded conventional ships for AI use. When we're not just playing with a Frigate vs. smallish fleets, Phase Cloaks quit being all that cool.
I've tried out various things to improve them, and I'm pretty sure that this works.
1. While Phase Cloaked, give ships greater speeds and maneuverability. How much? Enough to run away from things a tier down from you; i.e., Cruisers should out-run Destroyers but not Frigates. This allows Cloaked ships to get boxed, but not as easily.
2. Phase Cloaked ships should use Phase Teleporters as their System, preferably ones with a bit more range than usual (but a reasonable cooldown; I have mine set at 10 seconds). This allows them to achieve what we all want most from Phase Cloak- the element of sudden tactical surprise. Short of a Phase Cloak that grants true invisibility to LOS, this is the next-best thing.
There doesn't appear to be any way to allow Phase Teleporters a delay before "re-emerging"; this would be very useful, as it would increase the surprise value, especially if it was a bit random and the Ship did not exist to the AI until it emerged again.
But as it stands, this combo makes Phase Cloaked ships act like "space submarines"- alpha-strike experts who can get in, do some serious good (like knocking out engines or delivering a fatal torpedo) then get out before they get crushed, while running away when they get boxed (just like real submarines do). It also makes hunting them down a lot trickier than merely sitting and waiting for them to un-phase and then beating them to death; they have the choice of when and where to be in combat, making them genuinely useful in the hands of the AI.