I've just setup the London (my Excelsior) to be a dedicated STF/Borg ship and moved all my anti-proton weapons from the Argus (my Sovereign) to there. I then setup the Argus with all retrofit phasers and I'm currently working on getting some purple quantums on it. I also gave it my Ageis set and move the Borg set to the London too.
See, I used anti-proton beams all of the time at end level, but I've done more damage with a Phaser/Polaron & Quantum configuration on my cruiser. I don't know if it's my particular build, or if it's in my head, but I do some deadly DPS with my current setup, and I take them right into the STFs and blast away.