Thinking back on the Venom twist, I think the primary thing that ruins it for me isn't really part of MGSV at all Instead, but how the baggage from PW affects it. The point of no return for the MGS story is the PW story and how it taints everything that came before and after it, since 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.
Everyone loves the ending of MGS3, because on top of being intense and emotional, 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 not only unnecessarily filling in gaps that didn't need to be filled, but also completely erasing his original implied 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 affects my perception of V's twist as well as the BB storyline of the whole series post MGS3/PO. 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 could have been alright, but Kojima's apathy towards creating a consistent narrative caught up to him and I don't think that the lore can recover from that.