So me and a friend asked each other the same thing earlier today. Was quiet unmasked originally? Granted, she in mission 46 didn't look too much like the Quiet i got familiar with over the course of the game, but still I feel like I woulda been like "that's totally Quiet" the first time through. Also, did The Man On Fire look more obviously like Volgin the second time around, or was it just cuz I already knew? I swear at one point he was wearing his old uniform. I do wish there were more stark differences or something to give the second playthrough more meaning. Cuz yeah, it's a pretty boring scripted sequence.
You know what, here's a better question. Why the fuck did quiet walk into my room to kill me? She's a fucking super-elite sniper. I know this from first hand experience with her destroying entire bases single-handedly. Even if she didn't have the inviso-powers the wolbachia gave her. Girl's way more capable than the prologue would suggest.