For many fans, the separation of Hideo Kojima and Konami marked the true end of the Metal Gear Solid storyline. While that's not necessarily true, since Konami could just as well continue the franchise without Kojima's blessing, it's likely that the backlash would be severe. Kojima's long and arduous departure from Konami was painful to see, and resulted in the collective lambasting from thousands of Metal Gear and Kojima fans in general.
Alongside Kojima's unfortunate treatment and departure from Konami comes several side effects of the games he produced and directed, including the revered Metal Gear Solid franchise. It's no secret that Metal Gear Solid 5 ends abruptly because, narratively speaking, the game was never truly finished. This also means there's a whole lot of unanswered questions from the overarching Metal Gear Solid canon that were presumably meant to be resolved in Phantom Pain.
Metal Gear Solid 5's "True" Ending
Firstly, the gigantic elephant in the room has to be Metal Gear Solid 5's rushed ending and the missing "Mission 51." While the revelations of "Venom Snake" in relation to Big Boss were (and still are) meant to be the true ending to Metal Gear Solid 5, the truth is that the game's story was meant to continue beyond the 46th mission in the game. That much is made clear by the recreated bonus footage from the supposedly cancelled Mission 51, which has a ton of story-relevant moments between Big Boss, Liquid Snake, Psycho Mantis, and the remaining XOF forces under control of Cipher.
The mission depicts a final showdown between the phantom Big Boss and Liquid Snake's Sahelanthropus, which in its own right would've been a fitting ending for the game. That hint of Eli (Liquid Snake) and Psycho Mantis with the vocal cord parasite was meant to lead into Eli recruiting the child soldiers from Africa and heading back with Sahelanthropus, with nuclear weapons in tow. "Kingdom of the Flies" was to mark the end of the parasite and Sahelanthropus, but this episode never came to fruition in development.
This is why it seems like Metal Gear Solid 5 ends abruptly, because for all intents and purposes, it does. There was a clear direction the story was headed in, and the deleted "Mission 51" seems to detail this. Unfortunately, now those events are simply left up to speculation.
"Eyes on Kazuhira" May Have Hinted at a Long Con
One detail that's still vexing, also from Metal Gear Solid 5, is one of Code Talker's last lines in the game that seemingly goes on unanswered. "Eyes on Kazuhira, a message from the parasites." Some believe this message is a hint of Kaz's deception, that he's actually working with Skull Face to undermine Venom Snake and betray the real Big Boss. Unfortunately, the extent of truth in Code Talker's message to Venom Snake may never be truly proven, but it's a very likely scenario given the evidence and the story Metal Gear Solid 5 was meant to tell.
If Venom Snake and Mother Base was meant to be a diversion for Big Boss and the real Outer Heaven, then it's possible Miller was working with Skull Face to keep Mother Base and Venom Snake in check. The various elements of hypnotherapy that were implanted in Venom Snake to make them believe they were "Big Boss" was certainly hinting at that. However, despite how much potential evidence is out there, this theory still remains a mystery. While it's incredibly close, there's still several missing pieces to confirm that Kaz was working with Cipher all along, and wasn't actually working in the Diamond Dogs' favor.
"La-li-lu-le-lo," Cipher, and the True Identity of the Patriots
Away from just the mysteries left behind by Metal Gear Solid 5, there was one overarching villainous source to all of the conflicts and issues in the whole franchise: The Patriots. The Patriots are basically a giant AI super-network that rose to such supreme power that it dictated and conducted the actions of the United States. At first, it was believed that the Patriots were run by something called the "Wisemen's Committee," but as it turned out that wasn't actually true. However, the true origins of the Patriots have never been explained beyond being the "primordial soup, a base of evolution" of the White House, or essentially the technological manifestation of American morality.
Supposedly, the Patriots were formed between major players in the Metal Gear Solid canon to enact the will of The Boss on to the United States and the world. Zero eventually was seen as the figurehead of the Patriots, after Big Boss and several other members split from the organization over political differences on how to enforce the Boss' will. Zero supposedly then created the Patriots AI before being reduced to a vegetative state, but it's never explained how this supercomputer became so insanely powerful to literally control the United States.
For the record, the Patriots were powerful enough to: install a president (Solidus) completely under the Patriots' control, basically orchestrate and cover up the utter destruction of southern Manhattan after the events of Metal Gear Solid 2, and also implant nanomachines into every super soldier around the world and control "the war economy." The timeline doesn't exactly add up from rudimentary AI with hopes of unification to totalitarian super-network designed to control the world. These things apparently just happened under Zero, and that revelation may never come to pass now that the Metal Gear Solid franchise is effectively dormant.