Oh boy, another one? Ehh, I'm too tired of writing out well-constructed arguments. Simply put, if you are dissatisfied with the story SE is telling (or SELL[ing], if you want to be cynical), cancel your subscription and stop playing the game. That's how you get them.

Just cuz I'm bored...

Think you could have fought back as a PGL / MNK? Try punching someone wearing chain mail bare-fisted (all the Brass Blades). Now try punching someone wearing plate mail, again bare-fisted (the Sultansworn, who would have gotten involved if you started beating up / killing Brass Blades). Now, who got hurt more: you or them? (Don't say you would have grappled them. Everything except the Shoulder Tackle is a hand or foot attack - there are no grappling moves. When they include a Wrestler class, go ahead and whine about it.)

There are too many variables to account for every class. Some people have brought up the fact you're allowed to wear plate gloves but not a weapon in to the Sultana's chambers, and I've pointed out it's probably NIN who had the best chance of a nonviolent escape, relatively speaking. Savvy players wouldn't have taken Laurentius' oh-so-helpfully pointed-out vial. Savvy players would have left it with Momodi, or given it to Severian to analyze. Savvy players would have run up and down Ul'dah loudly proclaiming they met Laurentius out in Western Thanalan and he told us to take this extremely suspicious empty vial. There were simply too many options (and from the storyline's perspective we were rushed), so we had to hold ye olde Idiot Ball for a few minutes.

We're also not invincible combatants. In every Duty except some of the Discipline and Job quests we've got at LEAST one person backing us up. "But we've killed a bunch of Primals unlike those candy-ass guards!" you say? We're able to do that "easily" because we can't be tempered. Everyday people CAN bring down Primals, it just requires human wave tactics (look up how the Company of Heroes beat Titan and Leviathan). And we were unarmed, making everyone but PGL / MNK pretty helpless (and as I pointed out above, even they couldn't realistically fight back without a weapon).

Fighting back would also have given them legal grounds to arrest you. "But I'm a Chaotic Good rebel!" you say? Well, you'd probably get killed or legally jailed if you fought back, and I'd like to think the Warrior of Light is actually... you know... Good, not Chaotic Stupid (despite holding the Idiot Ball) enough to not realize when they'd been outplayed. Even Merlwyb, the leader most leaning towards CG (or maybe CN, being a pirate and all) had to be reminded by her aide they had to leave before things turned into an international incident and tore Eorzea apart; the Japanese version of the scene makes it clear she was about to blow Ilberd's brains out until her aide said something (or so I've heard).

Don't like how control of your character was taken away? Well, are you mad control of your character is taken away when you're having praise and adulation heaped on you? No? What's the difference?

... honestly, aside from being forced to take the empty vial from Laurentius I didn't think there was a huge hole in the story, and I enjoyed how it made us fallible even after all the praise and adoration that's been heaped on us throughout 2.x.