I've used my Negh'var for a long time, and I love it! I've got anti-proton beam arrays as the primary energy weapons, and the quad disruptor cannons from the Ning'tao class BoP on it as well. Quantum torps fore and aft for projectiles, and an RCS console to negate it's slow turn rate. I have a bortas as well, but the Negh'var is my choice for most missions, especially STF's.
To have more effective firepower, I suggest consolidating all your Energy Weapons to 1 damage type. Go all-in on either AP or Disruptors.
Between the two damage types, it seems you put alot more resources into AP weapons. I suggest ditching the Disruptor Quads and get some sort of AP cannon / DHC to replace it.
Consolidating to only 1 damage type allows you to slot whatever TAC energy damage consoles to the specialized damage type that offer higher damage bonuses. "Antiproton Mag Regulators" in this case. Generic warhead / beam / cannon / mine consoles have lower bonuses than the specialized ones, usually by 1/3 less.
The Negh'Var doesn't have the most TAC consoles, so you really need to maximize what you get out of them.