The best thing to come out of this game is the discussion. And the gameplay, of course -- that was 125 hours of gameplay that I enjoyed from top to bottom, possibly minus some overindulgence fatigue every now and then. The surely controversial ending at least gives me a whole lot more to talk about, even though as my above huge spoilers having nothing to do it with show that there's plenty to talk about even without it.
So here's an obvious thing that comes up when an ending is not to one's liking: How would it have been better? In particular, how could it have been better executed without changing its direction entirely?
As I mentioned in my initial reaction, I took the revelation hard. I tried to be as unfiltered as possible, letting the sheer rawness of my reaction out, and I hope it shined through as brightly as it burned within me. My reaction to the revelation was less shock and more a definite, bored "Are you joking?" followed eventually by a flat "What" when it became clear that they were not. But I also began healing quite quickly, and I take note of what helped, and have explored within myself what I think would have made that bitter pill easier to swallow, or might even have turned it into the kind of stealth brilliance I posited earlier.
I think much of my distaste comes from the fact of just how "Big Boss" was made. Even having him turn out to be a clone all along would have been better, which is why Zero describing him as a "memetic clone" eased my upset. If my character is going to be some kind of impostor of Big Boss, I want him to be at least as close as possible such that I can at least reliably feel like I was still playing Big Boss throughout the game. The problem starts with the fact that the manner of his "cloning" didn't sit well with me: Although the explanation of just how deep the process was helped me, it still wasn't the same as if Big Boss's very neuron patterns or whatever had been cloned into "John" (I gave him Naked Snake's real name from MGS3)'s brain through super-advanced technology, or if the Floating Boy's psychic weirdness had somehow been involved.
Another way the problem could have been alleviated is if the game had not ended there but instead helped me work through the process of accepting this. You can't just end on something like that -- it leaves me empty inside, feeling like everything I've played was a sham. Even if it isn't true, I still need to be convinced, to be helped through it; make it not the end, but a turning point, and put in that extra legwork to help us through our resulting anxiety -- in other words, more missions. My desire to continue the game is shot, even though the gameplay was so much fun, because now I've been left high and dry with nowhere for these feelings to go (but this forum, obviously) and just an empty world of mindless objectives with no story attached (and no Quiet!) remaining for me.
Another improvement, I think, would be to have the man "Big Boss" used to be be a complete mystery. I think that having his past self be a silent, nameless, faceless first-person protag would have had far more the intended "meta" effect than the mistaken effort that was asking you to craft a new appearance for multiplayer missions and expecting you to recreate yourself (when instead I gave not half a fuck and just named him John after Snake's real name in MGS3). (Also, even if I had recreated myself, said effect is ruined anyway by having him turn out to be the helicopter medic.)
Another way to improve it, which totally contradicts the previous suggestion, would be to go completely the opposite direction and have Big Boss's former self be instead a quite well-defined character, and not just in that he was some nameless medic. This one works best with the option where the real Boss is still played by Hayter. In redefining Snake by changing his voice actor, go all-out and have it turn out that far more of what we experienced of this Snake was idiosyncratic to himself
rather than a mimicry of another man's personality. Make him a true memetic offspring (as Sutherland's Snake is to Hayter's) by having everything about him that's changed that we had to get used to ever since Ground Zeroes turn out to be facets of himself rather than a change that is retroactively also true of the original, erasing Hayter's Snake even more than he's sadly already been.
Lastly, and I go back and forth on this one, maybe having the original Jack truly ride off into the sunset would have been better than the half-business that happened. Ocelot hands him a new identity and he rides off in civvies like he's going to live out the rest of his days as any other man only for it next to be said that he's just going off to do what his double was already doing, for reasons that still aren't clear to me. This option also works best with the option where the original is still played by Hayter.