I can understand the feeling of the game being incomplete from the lack of closure on the Eli/Sahelanthropous story just fucking right off, but the rest is pretty solid and well wrapped up when you realize TPP is just a tool to set up the time line as understood in MGS4.
It explains Grey Fox's absence, why he would go to Outter Heaven, and why he would be on Big Boss's side in Zanzibar Land.
It explains why miller would suddenly be present in MG2 instead of being part of Intrude N313, and makes a lot of sense on how Liquid and Ocelot would know about miller and want to kill him for MGS.
It shows how Big Boss descended into madness while also staying the greatest fucking saint in the world. Phantom Big Boss went renegade after that PTSD from the Quarantine chamber, while real Big Boss kept working in the background to oppose Donald Anderson's new Patriots.
Throughout all of this, it managed to do the twist reveal extremely well, the only shitty part was plying through that entire mssion again instead of breezing through or just doing the important bits. The signs were all there if you were looking for them: Ishmael's voice, abilities, and comments, Snake not knowing Russian which he was extremely fluent in (Which Ocelot tries to cover it up with a lie?), Phantom Big Boss had no real reaction to the Boss's voice, while real Big Boss would have had a PTSD attack, Volgin suddenly backs off when getting up close and personal with Phantom Big Boss because he realizes it's not his enemy, the DNA test was a 0% match for someone we knew was obviously Big Boss's clone.
Also, Quiet knew the whole time that she was dealing with Phantom Big Boss. She knew it wasn't Big Boss when she was sent to assassinate the real one, claiming the guy next to the real one saw her face and then proceeded to strangle him face to facel, getting a good look at the fact Phantom Big Boss had a damn horn. Years later, she'd fail to kill him again. He spared her, stopped her from committing suicide, abducted her, and was literally the only person to treat her like a human being on all of Mother Base. You have Lima and Stockholm Syndrome at work here, on top of Phantom Big Boss being a pretty decent guy all around, rich, powerful, charismatic, and supremely confident. They even work together a lot on the field sharing foxholes together so to speak. Hell, with all that I'd want to fuck the man too.
Overall, it's a great story that's true to the MGS themes. It's disjointed in its presentation, and left a little incomplete following the shitstorm at Konami. Just because it was told poorly, which was possibly out of Kojia's hands due to working conditions, doesn't mean you can't step away and appreciate how well constructed it is. TPP sets a rock solid foundation for future events, and had an ending that will stick with most of us forever.