So I'm finally listening through the MGSV spoilercast, and while I don't agree with a lot of their interpretations, their discussions have made me fully realize that I may not dislike the MGSV twist as much as I initially thought I did. Instead, what I actually hate is the PW story and how it taints everything that came before and after it. Basically any time Woolie or someone else was tying something in V to PW, I found myself getting annoyed because that's the game that ruined Big Boss/The Boss's characters and the overall plot. It feels like tying V back to PW legitimizes what that game did to them, which is ultimately what I found most annoying.
I love the ending of MGS3, because like they said on the podcast, it leaves you with all the pieces to the Big Boss puzzle. He is disillusioned with the world/government and so goes down a dark path BECAUSE of his reverence for The Boss and what happened to her. But then PW undermines all of that, by completely erasing that motivation and instead reintroducing (a fake) The Boss and having Big Boss completely regress as a character only to come to the complete opposite conclusion at the end of the game, when he this time REJECTS The Boss and decides he will now go on his dark path because for some reason he thinks The Boss betrayed him.
The fact that this new interpretation paints how you view MGSV is probably what most affected my perception of V's twist for me. I actually kind of like the idea of an older and post MGS3 BB being an asshole and unknowingly becoming what he hates by doing to Venom what the government did to his mentor (Though at the same time, I don't think what he did with Venom is exactly the same as what happened to The Boss). But when you start looking at this through PW's retelling of Big Boss's motivations, it just becomes way less satisfying. Now he's acting like a dick because he doesn't care about The Boss anymore and what was done to her, and he may actually be reenacting The Boss's manipulation somewhat intentionally. Without PW, I think the MGSV twist is alright (though the game and it's story still have a ton of other problems), I just wish we got more of them dissecting how much I think PW detrimentally affected the overall plot instead of them trying to tie PW and V together.