An addendum is that if you have one or two phase ships in your fleet, whether piloted by the player or not, the new AI behavior for clustering around one another as they "circle the wagons" cannot be underestimated for exploitation. They will voluntarily block one another's firing arcs in a large blob to better protect themselves against a phase ship.
They should only do that when there isn't much else other than phase ships nearby, though - is that not what you're seeing?
I believe it's working as intended! It's just fun to isolate a distant group like a sheep dog barking at the herd. It's very hard to do spontaneously in the middle of a big battle (needing advance scouting and planning), but I love that you created it. Watching the enemy fleet adapt to fighting primarily phase ships was a "wow, cool!" moment the first time I saw it. The change to phase combat tactics at a level below [HYPER REDACTED] is much appreciated, and I think it adds a neat tactic to the battles.
It can lead to some interesting alternate engagements early in a battle where you deploy phase ships as an advance force, during a staggered deployment, around the objective locations.
My phase ship allies, as noted by others, do sometimes make questionable decisions, unfortunately. I'm not sure what could be done to help them. I don't know much about programming AI, just the gist of weights and priorities. It seems like a challenging thing to do. A lot of phase ship combat comes down to reading the enemy and accurately predicting where to go, from where and when to fire, and how you'll escape afterward. There's a lot of nuance to consider, like enemy turret turning speed, fire rate and/or burst cooldown, your approach angle, your firing angle and position, and where you'll be shot - and by what. Because you'll almost definitely, eventually, be hit.
And of course the king of all considerations: making sure you don't overflux yourself and death spiral while surrounded by a pack of angry Hounds with Assault Chainguns. Or worse.
I'm impressed that the AI does as well as it does, all things considered.