Certainly guns and armor are important considerations in ship balance, and something we do take into account. However, if I can't get you in my firing arcs, then all the cannons in the world don't matter. Generally, our big picture view is: ships of the line can, with enough time, and if they get to go in a straight line, run down any smaller warship. Smaller warships can out accelerate and out turn ships of the line.
Pirates, like all MMORPGs, is a HUGE game. I don't pretend to know ever corner of it. So if what I'm about to say is wrong, please call me out.
My perception is: in a one on one fight a properly equipped and skilled privateer in an Master Craft Capricieux will beat a properly equipped and skilled naval officer in a Mordaunt most of the time (assuming roughly equally skilled captains). When Taelorn and I tried this several times, switching sides between attempts, we found this to be the case. The caveat is that right now, because the Capricieux's speed is too low (which is fixed 1.2), the Mordaunt can probably just set his sails and run away.
The second problem with that scenario is that it requires a 1 on 1 fight, which is almost certainly not going to happen to a naval officer in a Mordaunt. So where does this leave Privateers? In the dangerous position of trying to pick off one Mordaunt from a line of battle. This is a much harder proposition. We're hoping that some of the ship and skill tuning Taelorn did in 1.2 will help make this somewhat easier, but I'm prepared to believe that we'll need to do more. Certainly we will continue to monitor the situation, and make more changes as we see the need.
Finally I wanted to note that, for me personally, sailing ships of the line is boring. I don't like the experience. In battle, both PvE and PvP I want to sail a Frigate or smaller, so it's important to me personally that ships other than the behemoth SOLs are viable in PvP. However, the line of battle is a popular tactic for a reason: it works really well. This is unlikely to change, and fighting a line of battle is always going to be a challenge for non-SOLs.