So the new trailer came out and everyone is saying that this MGS5, which is believable. If this is supposed to be Naked Snake (BIG BOSS) where does this fit in the timeline? In MGS4 where Naked Snake dies he is not missing an arm... so how does this work? This is just a simple question. Any other tie in or things you have noticed please let them be known. 

Kojima has a knack for unbelievable storylines, so I'd say it's the fusion of Old Snake and Big Boss reincarnated in 1978.

I think it would be a strange decision letting a small unknown developer (Moby Dick Games or something) develop such a big game. Only Capcom thinks that's a great idea.

Ocelot loses an arm, right?

the right arm.

Unless... they are not a real studio, just a symbol of how Kojima is Ahab and Metal Gear is his white whale. Dun dun dunnnnn!

the game has lots of similarities with Ground zeroes regarding the equipment the soldiers use. So I think it should around that time in "history". By the end of the trailer you get to see a kid floating => Psycho Mantis.

What I think is happening is that BigBoss has been captured and they are using the powers of Psycho Mantis to dive into his mind and get some information, and all what is happening about the whale, the flaming Pegasus and the killing is only happening in Snake´s mind. The one bandaged is the dude from the ground Zeroes trailer, and maybe in that illusion Psycho mantis is making him help snake so that he trusts him, and give them the information they want.

The arm thing most probably refers to something that actually happened in the game. Maybe he broke his arm before he was captured, so in the illusion it is like a prosthetic arm because he can not use it.

Deep 

I would say it's set right inbetween Peace Walker and Metal Gear 1, something to do with the Les Enfants Terrible project and Big Boss getting on the bad side of the US government.

My guess would be right after Ground Zeroes. Kojima did say that Ground Zeroes will be the prologue to a future game, I believe.