So hypothetically, what would Chapter 3 even be about, since so many are talking about it?
Honestly, at the end of Chapter 1 I was like "uuhm, so the central conflict is kind of resolved now. How can this continue?" and Chapter 2's actual story missions are pretty much just a series of closure for each supporting character's subplot.
And last but not least, I think people are wrong in that they think the missing Phantom Episode is "the real epilogue". I disagree. There's totally content from the game that was cut, but it wasn't the actual ending... it was the buildup to it.
As it is, and as was excellently pointed out in
George "Bunnyhop" Weidman's analysis, mission 46 just... appears. There's no plot that leads into it. I'd say the missing story content from the game should've simply closed off the remainder of the character subplots (Eli, Miller and Ocelot) and then signified Snake reminiscing over his awakening that would lead the player to discover the twist.
The ending itself is just fine, and to me the meaning it has is that MGSV is honest about the fact that its main focus is letting the player have fun with the game. You know Kojima's been running out of ideas as he was constantly forced to keep making these games that he intended to conclude so long ago, and in that sense I found the ending to be amazing for this one. It neatly makes a statement about player agency and it explains why MGS V had so little interesting story in the first place, and the marketing about Snake's journey to the dark side was mostly a ploy akin to MGS2. This is the part where I don't share my opinion with George Weidman, as I think it's perfectly fine the way it is. It's only a shame we didn't get the actual chapter 2 that was intended, but the beginning, middle and end of this game's campaign is mostly intact.