You lose nothing by taking the extra Proc, even without any investment into Flow Capacitors... so Polarized Disruptors all the way for PVE. If you're gonna go the PVP route though, it's pretty much Phasers for the chance to disable shields.
Originally Posted by verkion
Is there a detailed comparison of APB3 vs. the equivalent 3rd level Cannon skill? i.e. Is it better to equip CSV3/lower APB or APB3/lower CSV?
Note that as-per the above conversation, APB is affected by the whole Damage Resistance Diminishing Returns mechanic. Under a best-case scenario you can still deal 50% more hull damage whenever you use APB3, but on average for an unbuffed enemy (one with no damage resistance) after DR it'll work out to about 33% more hull damage. Remember though that this is applied to all damage sources hitting the enemy you shoot at - Teammates, Pets, Torps, Energy Weapons, Warp Plasma DoTs, Gravity wells, etc. etc.