Does anyone actually want the AI to properly use phase ships/hyperion? That sounds awful, getting one shot with no counter-play. The whole concept is not fun to play against, I'm totally ok with the AI being bad at using them. The alternative is much worse.
Hyperion does have counterplay, player just never really needs to practice it.
First of all in Paragon vs Hyperion scenario, Paragon could just refuse to drop shield. Hyperion can't really build up hard flux on it, wait it out or anything else. A 360 shield that powerful stops it completely.
Even simple non-360 omni shield could stop it. You just need to keep shield down and reaction-raise it as Hyperion jumps (it sounds more difficult than actually is).
With just forward shield - sure, alone you can't do anything. But multiple ships could form up back-to-back, which would at the very least complicate Hyperion's job (and actually stop it, if they are close enough - can't jump into other ship's collision radius).
To win you don't really need to kill it. Just preventing it from killing you is already a win by CR.
So, yeah, I'd like AI Hyperions to be competent. It costs like a cruiser, it should be at least a comparable threat.
As a side note: Hyperion vs Hyperion fights are like wild west duels. Jump behind enemy, as they try to jump behind you. But AI is very predictable and has large delay on sequential jumps, so this gets old fast.
Stopping current Afflictor with QD is actually more difficult - because QD shuts down most of your options. But Afflictor will lose QD in next release anyway.
At which point smarter shield management + accelerated shield might be just enough (can't really test it against current AI...).
Well, invulnerability frame kill may be a bit too good too, so maybe nerf that to oblivion as well.