The story is just as complex as MGS2's and touching upon a large number of topics important to canon: like talking about the persistence of one's will and the inception of the idea to control society through information.
* Who created the Patriot AI's;
* How did the world change in order to accommodate the Patriot AI's
* How did Big Boss survive Outer Heaven's destruction;
* Why was the Big Boss from MG2 so differently portrayed from the one in MG;
* The reason why Ocelot was so eager to believe S3 meant Solid Snake Simulation instead of its true meaning;
* How did Psycho Mantis, Liquid Snake and Revolver Ocelot were involved before MGS;
* Who killed Miller in 2005;
If more content is released, great: this game is amazing and will only get better. But I'm satisfied with what I got. A lot!
The thing is nobody was really asking these questions. Particularly:
* Who created the Patriot AI's;
We knew it was DARPA, given the involvement of SIGINT into DARPA at the end of MGS3, and given their control of the internet. The extra detail of Strangelove being the particular person to do it is irrelevant, given how she wasn't conceived until after MGS4 was released.
* How did Big Boss survive Outer Heaven's destruction;
Nobody was really asking this,
* The reason why Ocelot was so eager to believe S3 meant Solid Snake Simulation instead of its true meaning;
Everything Ocelot did in MGS1 to 4 is super suspect. Whether he believes the S3 name or not is kind of a super minor point
* How did Psycho Mantis, Liquid Snake and Revolver Ocelot were involved before MGS;
MGS1 just says that they were part of Foxhound; we receive no indication that Mantis had a long relationship with Liquid or Ocelot, other than Mantis saying "you are worse than Liquid" (or something to that effect) to Solid when he died. Liquid does not intimate he knew Big Boss or that he had actually drived a metal gear like robot in his childhood either, or that he knew Ocelot from old times. Before MGSV we receive no indication Liquid and Mantis knew each other from childhood.
edit: MGS1 liquid says
"Snake : ...So that's why you're so obsessed with Big Boss. Some warped
kind of love.
Liquid : Love!? It's hate!! He always told me I was inferior and now I'll
have my revenge!! You should understand me, brother. You killed
our father with your own hands! You stole my chance for revenge!
Now I'll finish the work that father began. I will surpass him...
I will destroy him!"
Which is doubly weird because we don't really see this happen in MGSV either!
* Who killed Miller in 2005;
I assume this means "who directly killed Miller", as in, who is the assassin.
While some people are actually curious about this, MGSV doesn't really say that it was Ocelot. We are exactly in the same place as in MGS1 about this.
Post MGSV, this quote from the MG2 wiki caught my eye:
It is possible Miller grew bitter in time about having been fiddled one more time about Venom's identity. That and BB actually creating a mercenary nation with nukes probably drove him over the edge to hating BB.