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So I'm basically through it (through the whole story anyway) and... I'm not completely turned around, there's definitely a lot here that should have been done differently, but it's effective and I will grudgingly admit is in a lot of ways the bridge that the Big Boss-era games needed to Solid Snake's era.
First, the bad: I do not feel ashamed of my words and deeds and I was glad to have finally been able to invent clothes for Quiet. Honestly, it rules that MGSV opened up acting roles for Stefanie Joosten, she is legit a hell of an actress and manages to convey a lot with just her motion capture and humming. Even so, uh... Yeah. There's a repeated theme throughout both GZ and PP of women being fridged, almost always after being subjected to sexual violence, which is fucked up and gross in its own right and undermines Quiet's big sacrifice (which is arguably fucked up in its own right even without that context because if it's read as part of V's thematic thread of loss, and taken as a piece with her tape, it comes across that Quiet condemning herself to death by parasite is Venom's loss, not her own!)
The whole shit with Paz is just gross and bad and I don't want to relitigate it. The sequence on the medical platform is... effective for what it is but again, Paz is only there for Venom to feel Some Kind Of Way about. Yuck. I am going to kick Hideo Kojima directly in the taint.
Kiefer Sutherland should not have been cast over David Hayter. They could have done something cool if David Hayter had played Big Boss and Kiefer Sutherland had played Venom but they didn't and it sucks and Kiefer Sutherland really only hits the right tone once in the entire game, in the cutscene after Shining Lights, Even In Death.
Now the good: It really feels weird at first that the big victory over Skull Face caps off chapter 1 and then the player really gets the same dawning realization that nothing is actually over that Kaz comes to. The emotional climax of the game is Shining Lights, Even In Death and it is really effective. Everything after that is falling action, and it does leave one feeling like there's no thematic place they could have worked in episode 51 even though without it there's a massive dangling plot thread. Liquid and Mantis leaving with Sahelanthropus and just vanishing is thematic in its own right in terms of bridging to MGS so even that works okay.
Huey being the real villain of the piece works fantastically well and is honestly an incredible payoff; Huey is arguably the real villain of the entire series, even moreso than Zero or the Patriot AIs, and the game is acutely aware of this and hammers it home hard. People who say there's no "start of darkness" for Venom really miss the point: Venom was never evil - the end of Shining Lights arguably shows Venom as the hero and father to his soldiers that Big Boss never truly was - and the "villainy", such as it is, was Big Boss's and Ocelot's and most immediately Huey's. Kaz and Venom are surrounded by villainy in the form of betrayals by everyone they trusted other than each other, and ultimately Venom's nature is a final betrayal between them too. In the end, they have nothing and have lost everything. Venom is just a shadow and Kaz is really left with nothing but a gnawing need for revenge and wounds that will never heal. It retroactively turns Miller's "replacement" in MGS from a kind of weird stunt twist that didn't mean much to anyone who hadn't played Metal Gear 2 (ie everyone outside Japan) into a real stark mirroring of what Big Boss did to Venom, and the fruit of Big Boss's legacy finally taking the last thing Kaz had left, his life.
In the words of @ChipCheezum, "It was the best of Metal Gears, it was the worst of Metal Gears."