Let's consider what could stop a player piloted Afflictor from taking out a ship within enemy fleet:
- an enemy Afflictor or Shade, perfectly tailing me to attack right as I unphase. A tag team of two could do it even with disadvantages in character skills and variant.
- Harbinger, denying area around the target (since it can force me out of phase).
- Doom, dropping mines in spot I'm most likely to attack from (right as I prepare to unphase behind target). Even reactive usage of mines as now is dangerous, but doesn't really stop Afflictor.
- Tachyon Lances, Phase Lances, and to lesser degree HILs (long initiation) and Heavy Blasters (dodge-able) leading the me to attack on unphase.
- Keeping 360 shields up all the time for isolated ships. Huddling back-to-back for non-360 ships, also with shields preemptively raised.
- Self-defense abilities like phase skim or teleport. Phase cloak doesn't count because obviously I'd attack during cooldown.
- Fighters can force me to waste me some flux/time, but ultimately can't catch 200+ speed 4x time cloaked Afflictor.
And the most dreaded threat - enemy death explosions, though they obviously don't save the victim ship. I'll probably make a mod to draw these at some point. With cruisers and capitals the margins are razor thin, so it's very easy to attack from too short range by mistake.
Anyway point is - there are some things that can be done to protect fleet from an Afflictor, but they all take significant effort. And AI simply doesn't process it as any special threat (despite the fact that it is). Which leads to Afflictor game-play being too one-sided.