The story had its issues, primarily in pacing and the fact that it was incomplete. My biggest ones were:
- Too much detail on the copulating parasites. I'm fine with the weird nature gives superpowers concept, but honestly, the parasites drove all of human evolution? Fuck that. IMO, Code Talker is just a crazy old man with some wild ass theories. It's not like anything he said could be proven anyway.
- Not enough Skull Face. In GZ tapes,. Skull Face was damned terrifying but he was pretty much a non entity in TPP, we really needed more interactions with, him, a boss fight, anything.
- No fall. Yeah, we see where things are going, but there is no way around the fact that the marketing for the game was a complete lie. We don't see Vanom's descent into madness, and we don't see Big Boss' fall (it seems like he's already there). I think part of what has people so pissed is this, essentially the end of PW WAS the fall of BB. This is another story, the building of the legend.
- The best scenes in the game were spoiled in trailers YEARS ago. It made scenes have far less impact than they should have.
However, even with all of those issues, I still actually really liked the story.
Venom is a great MC. He's clearly different from BB, but I thought his characterization was damned good. Venom is in the situation he was in because he failed to find the second bomb in Paz. His mistake nearly caused BB's death, he feels that he also let a girl who he clearly had feelings for down (seriously, there are Paz posters all around, listen to her tapes again, Venom had the hots for her.) Of course, she was a dead woman anyway, but Venom didn't know that at the time.
That's not all. His failure lost him 9 years of his life, nearly killed BB, and killed any chance of rebuilding MSF. He was BB's best soldier and he still messed up. Even after he loses memory of who he was, that failure haunts him.
Venom wants desprately to be the hero. He wants to save everyone, and rebuild what he had in MSF. Sure he thinks he's BB, but he really is a different character. Look how he responds to people, look at what he does. The Paz scenes are heartbreaking, the stuff with Quiet as well. Venom routinely ignores the advice of his best men when it comes to saving others, he takes in the kids, he doesn't kill Quiet.
His defining moment in the game was when he had to stop the outbreak. And once again, fails to save anyone. It's the actual climax of his journey in the game we got, and his reactions were gold.
The problem is, that we don't get to see the end of this plot thread in the game itself. Mission 51 would have been the perfect end for him, shooting Eli, then finally saying fuck it, and leaving him to die due to his own stupidity. At that point, he no longer cared.
Huey's stuff was great as well, as it showed a descent into madness, and having such an incredible ass be so similar to your best bro in previous games really worked. And it had the added bonus of knowing that his son would eventually bone his next wife, and drive him to suicide.
Quiet's stuff was also strong. She was by far the best new character in the game, and her final mission was heartbreaking.
In the end though, the overall story the A to B to C of the plot wasn't what the game was about, it was about the characters, primarily Venom, and I thought it did a great job with far less intrusive cinematics than previous titles. Could it have had more? Clearly. But after the excess of MGS4, I was kinda happy for the attempt at subtlety.