There are so many, I'll leave it to three different ones though:
3. The fate of Eva
So let me get this straight, Eva is so obsessed with Big Boss that she is willing to throw herself on the pyre of his remains, thus burning herself to death. But she doesn't notice that it's clearly NOT Big Boss, because you know, wrong missing eye? Really? Not a huge fan of the can't live without my man trope played straight, but holy hell that was dumb.
2. The Naomi stuff, pretty much all of it. Ok, her creating the Nanomachines, and suping up Vamp, not so bad. Her having cancer, and using Nanomachines to keep herself alive, I get it. But her suicide literally made no sense. At all, and that's not getting into the BS with the FOX die. sonicmj went into that better than I could so I'll quote that post here:
Naomi tells Snake that he's a walking biological time bomb about to destroy the entire human race. But she realizes later that she's wrong and he'll be fine. She doesn't want him to kill himself. How does she solve this problem? Not by telling him, that's for sure. Instead she kills herself to atone for her horrifying sin of curing cancer. She also records a message for Snake to see after the FOXALIVE virus is uploaded that does not include this information. Then she makes plans to revive Big Boss, who has been kept alive in a coma for over a decade because reasons.
As a man of action, Big Boss knows what to do to make sure Snake lives. He has to go get The Boss's Patriot gun. He also has to go fetch Zero from whatever old age home he's being kept in. He has to take his gun and Zero to a graveyard just in time to stop Snake and deliver the good news. Then he kills an old man on life support in the late stages of dementia before Snake's eyes for entirely symbolic reasons. Finally, Big Boss dies from the FOXDIE virus that he knew Snake had, which the Patriots had implanted in Snake to kill Big Boss. Because the revival of Big Boss was apparently something they had predicted.
I feel like there must have been a better way convey this message.
in any other game, this whole chain of events would be the most absurd plot twist, in possibly the history of video games. I mean it really is that flat out absurd. It is only saved marginally for giving us the most distilled form of the Otacon crying like a little bitch scene of all time. I mean it, the first time I saw this scene I couldn't stop laughing for minutes.
Otacon's Life sucks
I think it's the "why does it always end this way!" that gives me hope that that entire scene was self parody. If so it would be brilliant.
1. Ocelot the Hero. Like others have said the whole Ocelot arm plot was stupid. It sucked then, it sucks today. I think what I find so offensive about it isn't the fact of the arm switcheroo, that is dumb, but well within the realm of MGS bad writing. No what really got me is the attempt to play up Ocelot as a hero. THe hero of the series in point of fact. Fuck that.
No really, fuck that. Ocelot is NOT anywhere near a good person, and has never been one. He's a horrible sadist, who let us not forget rapes Meryl in MGS 1, and kills her in the non-canon timeline. He gets off on torturing Snake, betrays everyone he has ever worked for, and is an overall ass. He's a great, badass villain, but no, you don't get to cast him as a hero in an info dump by Zombie Big Boss at the end of the game. It's insulting.
OTOH best plot twist in the Metal Gear Series? Right here:
Nanomachines, Son
