You cant expect AI replace player with any ship loadout.
I don't expect AI to replace the player. That said, there
are ship loadouts it can do pretty well with - the one I linked, for example, is halfway decent when it doesn't get swarmed with fighters while engaging larger targets (just fighters on their own it has no trouble with). It could still be halfway decent
there if it just had a bit better targetting priority - priorities I would like to be able to give it; the phase beams are
there to be anti-fighter weapons, and it's annoying to watch it try and use them against a shielded cruiser.
Even if it didn't aggressively finish off fighter wings (which I don't expect it to), simply using the anti-fighter weapons it has would lead to the last wing to disengage usually dying - a much better situation than it's in now.
The rest of the stuff you went on about - venting, and kinetic weapons, and omni shields - are all irrelevant to my example; there's only one non-fighter enemy ship that will actually try to close, the Apogee can't carry kinetic weapons (aside from maybe a few sabot SRMs, but those certainly won't help it against fighters), and the Apogee doesn't have omni shields. You might, if you want to discuss those things, consider a new thread.