The Pacification isn't what is preventing me from getting dummy like parses on A3S, though I might note that I do get parses like that in the first few phases.
The problem with A3S is that once I have to tank things I have to play a little more defensively to survive. I can get off my Fell Cleaves during the Hand of Pain DPS check, but even then I frequently see my health going down to a couple thousand, and I'm forced to go back into Defiance as soon as it's cleared.
You're not really forced to go into Defiance, since there's no real mitigation built into the stance. Not like DRK or PLD, anyway. You can also self heal and roll cooldowns to make it so you don't drop that low. It depends on how your healers are approaching the situation but if you ever feel in danger of dying I can guarantee one of two things happened/are happening:
1. Healers aren't being trusted
2. Cooldowns/Mitigation were not used properly.
Secondly it's important that your group works like a group and not like a gathering of individuals (protip: this is the main reason pug groups can suck outside of not knowing how to play their class to a minimum level). You need to know how your healers will heal you in what situations. You need to know when the Ninja is dropping Trick Attack, when the Bard is playing Foe Requiem, and when the tank will pop cooldowns and what the rotation will be. All of these things, and way more of the ilk, are what separates good groups from great groups, imo. Everyone needs to be on the same page and from your anecdotes my guess is that you guys aren't.
Berserk thing is silly too since you can click it off early if needed. A couple of seconds clicked off of Berserk >>>> holding it for a length of time.
Also no, DPS during add phase is one of the least important times to be DPSing in the entire fight.