If you're using it for support, under AI control... I'd probably go with something similar to its base variant; HIL & MIRV with secondary weapons optimized for an anti-fighter role, probably phase beams & burst PD lasers.
The AI doesn't do well with a plasma cannon in a hardpoint; this is indubitably true. For whatever reason it's vastly more accurate with a turreted plasma cannon.
Cerberusti and I are both talking about using an Apogee as a flagship, where the player can leverage the plasma cannon's high DPS & per-shot damage to devastating effect. And, well, you don't actually need flux-efficient weapons if you can dissipate the flux they generate; an Apogee with 30 vents can sustain plasma cannon fire almost indefinitely even with shields active. (And, once you've got some skill points and things like stabilized shields, it *can* sustain that indefinitely.)
The real key to making a usable plasma Apogee in early game is that you don't want to use all of its weapon slots. Fill in the turrets with support weapons, install a plasma cannon, throw everything else into vents and capacitors and targeting core hull mod and maybe unstable injector if you've got ordnance points to spare; you should come out with at least 20 each of vents & capacitors.