Why Chapter 2 makes sense and is well written
Since its release, many people have been claiming that chapter 2 is empty, badly written, disjointed, or an afterthought from the devs. I will show how that's not the case, and how it was crafted with clear intent.
Part 1: The Plot
From its very first cutscene [picture 1], we see that the core theme will be internal suspicion and paranoia. The void left by Skull Face (or Moby Dick's white whale)'s death, will prompt Miller to start an orwellian policy at Mother Base. This will lead to the departure of almost all the characters we've recruited (Quiet, Eli, the Mbele children, Huey) and to the deaths of a large chunk of our soldiers.
These events are not a coincidence, it's the central theme of the chapter making itself apparent, and it's all pretty consistent. This is made totally clear by the tapes [pic. 7] [pic. 8]. Here the writers link the themes of parasites, suspicion, racism, revenge and political control all together.
If we investigate mission 43 "Shining Lights", we see through optional radio calls (which probably 99% of players have missed) that Miller was responsible for that event [pic. 9]. That hatred turned inwards after the dissapearance of the external enemy is a consequence of revenge, and is one of Skull Face's parting gifts.
Mark Twain's quote used in the E3 2014 trailer summarizes it best: "Anger is an acid that can do more harm to the vessel in which it is stored than to anything on which it is poured.”
This self-hatred is also evidently showed in the Paz cutscenes.
The game also links that theme back to The Patriots, and how essential it is to define or fabricate an enemy in order to keep any group under control. Outer Heaven is no stranger to that logic.
Part 2: Game Design
With this clear red lining for the plot, we can see how most of the story is going to take place in the background, on Mother Base, and not on the field. The few new main ops have the purpose of showing us that even after Zero's dissapearance and SF's death, the cogs of the machine that is Cipher keep turning (mission 32 with the secret XOF assassin that comes if you wait for him, mission 35 and 41, etc..). Those cement the so-called "War without end" that BB and his men are in.
As for the main side ops, they're there for the same reason as the Zadornov missions in Peace Walker, they allow the game to reveal the story and tapes to us bit by bit, and give time for the things in the background to unfold.
Given the open world and RPG aspect of the game, that time is also necessary to allow the players to discover the optional cutscenes they may have not gotten yet (most importantly the Paz ones, or the ones related to the buddies, etc), and to improve their stats.
The game took its non-linearity to heart and offered a giant puzzle that the players can complete by replaying and exploring any of its parts freely. This might have been a problem, if we weren't given a fascinating lore and one of the most fun gameplays ever. Those two elements make that process worthwile.
Part 3: The Truth
The themes and the gamedesign offered to us by chapter 2 make us truly take the mantle of Big Boss by allowing us to fully develop our base, nukes and all, and also to make us go through a kind of initiation ritual, a plunging through the fires of hell that is very similar but even worse than the murder of The Boss, like an eternal, looping curse. This applies whether you consider BB and Venom to be different characters or not.
With the ending, Kojima cements this by finally giving us the keys to the franchise, packed up in a perfect loop, and to our own Outer Heaven. He even allows us to defy the canon of the franchise and of history by letting us the choice to rid the world of its nukes. "We can change the world - and with it, the future."
Part 51: The Missing Link
As for how the Truth is unlocked, nearly no one knows about this, but the ultimate requirement is actually listening to the tape about Eli's DNA test. You can do everything absolutely else in the game, but if you didn't listen to that, the mission won't appear. I even tested this by having it be the last yellow tape I listened to, and then by leaving some other ones "unlistened". Try it yourself.
This implies that the DNA test is what chronologically made Venom realize his true identity, and the same could be said about Miller. So even the mission's sudden appearance makes sense, though it's to be understood through the non-linearity of the game and how the players need to look for all the info.
TLDR:
The game's writing, game design and secrets make it clear that chapter 2 was crafted to be this way and that the whole thing conveys clear points that the authors wanted to make and themes they wanted to explore. Something with an intent that clearly defined can't be called unfinished.