Having finished the game myself I think a lot of the problems with the ending come from inconsistent overall writing (which looked at on a quest by quest basis is still strong).
As I commented in a different forum the game feels like there are two distinct ideas that got mashed together for the end product. You got V's story up until the heist and Johnny's story. To me it feels like these originally were two different games. V's story doesn't need Silverhand at all and is perfectly set up for itself. Dex is a legendary fixer and the heist goes wrong as normal. Dex then takes the biochip and screws you over, but you escape alive.
You then have your villain set up, but since he is a legend in NC you need help to get your revenge. Even if you are not out for revenge you still got Arasaka hunting you for the death of Saburo, so you need to at least get the chip (which could just be the engram of Saburo instead of Johnny) back to get out of that mess. You can then ally with the "lesser" fixers through working with them, you could ally with the underutilized gangs (pretty much only Maelstrom and the VB got some meat to them, Mox are pretty much non existent and Animals and 6th Street as well as Tyger Claws are mooks to shot, you could ally with the Nomads, you could use whatever caused the 2 year absence of Dex from NC and you could even ally with Arasaka. All options could lead to distinct endings and choices and the whole set up is there for a choice based RPG.
Then CDPR got their hands on Keanu Reeves and Silverhand goes all Shining on V's story as it's been set up to this point (Here's Johnny!) Still this might just be a personal feeling.
Speaking of the game we got, how do the engrams even truly work? As far as I understood it they upload the psyche to the engram and then implant that psyche into a new body (either a deceased or a clone or sth.) who will then continue to live as you. Your original body and psyche dies in the process.
An entire different question and can of worms is why Arasaka keeps an unchanged engram of Silverhand around. It is heavily implied that Arasaka would use the secure your Soul program to change the rich subtely to better suit their needs through the program. Why they wouldn't do that with Johnny is beyond me. That is kinda like the US Goverment keeping Bin Laden around for shits and giggles. But back to the engrams itself.
Do the engrams come with a healing factor? Because I would think that getting shot in the head by Dex and thus having a hole in your brain could impede the engram actually working and you don't have Arasaka pumping millions of eddies into you to fix that (you're dropped in a dump after all). Hard to overwrite something that's lying in a hotel floor.
But even if you look past the wound miraculously disappearing, why would your psyche even come back at all? You are dead and a corpse so the engram should have just uploaded Silverhand's psyche and that's that. Silverhand is back in full. There doesn't seem to be an explanation why V's psyche returns at all and causes the whole story since that is not how engrams should work.
And given that Engrams remodel your body/brain (which in iteself is weird because you are both human and thus should work perfectly well in a human body, especially given how easy you can swap body parts in this future) for reasons unknown and are supposed to work on deceased or clones and the body is fully yours to begin with, shoudn't your returning psyche just kick Johnny out immediately? Otherwise they could just use a random engram on any of the enemies to "erase" them in a form of psychic warfare, which in itself could almost carry a story.
Which then brings us to the endings. First in the Arasaka ending, Arasaka could easily give you a new body and upload your engram. That is the basis of their whole secure your soul thing after all. You can still imply they change you for the "devil's bargain" ending but you should be fully alive and not dying in that ending.
And in the 6 months left endings, where does that even come from or is hinted in the story at all? You got Silverhands psyche out of you and only your own engram left. Shouldn't this engram do the exact thing Silverhands engram did and remodel your body/brain back to V's original thoughts? Especially given that your engram has almost 60 years more of development? If Silverhand can rewrite a body with a hole in the brain, why can't your engram rewrite a perfectly healthy body? Which still leaves you with the moral dilemma of having used the Soulkiller.
As for the whole Real V vs Clone V thing, shouldn't Real V have died long before Mikoshi due to being shot in the head? Engrams only start up when used on dead bodies after all. So what you play throughout most of the game is already sort of a clone/engram version in my eyes.
Would have loved to just have an ending where you suvive (preferably without being soulkilled) and just have a short clip of an Arasaka board meeting with you showing up in their fiscal report as V-related losses of the Quarter. You will not stop Arasaka (since that is kinda the premise of Cyberpunk that it's more or less too late and in that regard a futile struggle) but you still get the feeling that you are a thorn in their side as you ply your trade with your friends.
Loving the discussion though and feel free to correct me on my assumptions.