One more question - Does Zero ever appear visually or is it just audio? I assumed audio since he seems to be mostly gone by the time you wake up.
Oh, and I haven't have a single word about Mantis, and who/what he is. I thought they would say something but it's not even clear if anyone but Eli can see him. Did I just miss it?
What I can't quite get my head around is the idea of perspective and how BB didn't deserve his bad reputation. I've read people saying it was Huey spreading lies but at the time of Metal Gear 1, BB had a good enough reputation to be in command of Foxhound and mission Intrude N3 so what rumors would he have spread if BB was still trusted? I guess it dances around Zero not being there anymore but even then I don't see how and why he was magically allowed to come back to FoxHound and lead a mission for Solid Snake.
It also leaves us with the whole Liquid snake being told by BB that he was inferior, since Phantom BB doesn't think Eli is a clone and real BB never interacted with him. It's also not clear if Phantom BB launches Outer Heaven as a revenge against real BB or something he thought BB would do. They basically both did the same thing for MEtal Gear 1 and 2, just at different times and the objectives seemed similar enough.
Major Zero appears exclusively in the 'truth' tapes post-Mission 46 as the end credits simply acknowledge his voice actor.
Ocelot speaks quite heavily about the young Psycho Mantis in several cassettes later in the game if I'm not mistaken. There's even a tape where he explains his psychogenic powers and outright states his abilities were triggered as a result of Big Boss/Venom Snake's awakening. Everyone can see him as it's stated somewhere, for example, that Skull Face convinced Mantis to join forces after his resurrection of Volgin disrupted XOF's assassination attempt in the prologue.
In regard to Huey, I don't believe it has been officially revealed what his actions were following his exile from Diamond Dogs. Miller simply speculations that he'll run around spreading negative word-of-mouth about their organization. It wouldn't be surprising if a future installment explores that he went back under the wing of The Patriots/Cipher to continue his Gear research. However, it stands right now, Ocelot's foreshadowing comes to fruition after he blends back into civilian society and, eventually, discovers that his son, Hal "Otacon" Emmerich, had an affair with his second wife. Perhaps in combination of guilt over his actions from
MGSV and this marital revelation, he simply drowns himself in their home pool nearly taking his daughter, Emma, in the process. Big Boss and Miller folding back into Foxhound hasn't been officially explained either and I'm guessing that'll be baggage the next creative director will have to potentially flesh out. My speculation at the moment is that he probably wanted to his train his genetic clone, Solid Snake, into hunting down Venom Snake once the Outer Heaven Uprising goes down. He might've additionally rejoined the U.S. government to adhere to the famous Sun Tzu quotation, "Keep your friends close, and your enemies closer," as a means to remove the heat off exposing Zanzibar Land as his true master plan.