The disruptors are lower down on the skills so they would be easier to spec heavier into them. But some of the other weapons like plasma have secondary effects.
You've essentially answered your own question. That's the tradeoff.
The Phaser and Disruptor skills (or Photon and Quantum for projectiles) are lower rank skills. So it takes less points to max them out...versus, say, Plasma, Polaron or whatever.
And the max skills give the same boost to their respective damage type. So the main advantage to the other weapon types is the different secondary effects. But personally I kinda like the basic phaser and disruptor procs - they're not bad.
That said, phaser and disruptor weapons are obviously more common. So for PvP purposes, I guess you might worry about running into opponents with disruptor resistance consoles...but not many people bother to gear for weapon damage resistance anyway. So.
The purple epic gear in Borg space is all Antiproton stuff... but as a Klingon, you'll probably be relying mostly on PvP reward gear, which compares favourably with the purple epic PvE stuff. So that's not really an issue.