Yea I think the Quarrel/Mangler has always been one of the best ships (probably the best), even in 5.5. You just need a bit more team support to fly one effectively now.

To get the same number of Kills and assist I need about three times as much damage on a gunship than I do on a Protorp equiped strike fighter. I blame the shield piercing of the Protorp for that, because with the gunship I have to break through the shield by dealing damage, which give them the chance to regenerate the shield when they are able to break LOS, while I don't have to do that on a Protorp equiped strike.

While this is true, the true value of ion railgun doesn't show up on the scoreboard. That slowdown effect really helps your team score kills. I'll often tap a target with ion railgun to apply the slow, and then moments later I see that pilot explode from a protorp. Had I not applied that slowdown effect, the enemy ship may have been able to just escape behind LoS.