Regarding your second point, what happens is that Alt uses Soulkiller on V when he // she submerges into the ice cold water. This means that V died and has been assimilated into Alt's AI, but Alt had returned a copy of V to inhabit his // her body (This is what we were talking about when we said Fake-V and Real-V. Real V is dead, Fake V is around for 6 months).
It just feels wrong to have not included at least one good ending. It doesn't necessarily have to be "happy" per se. I'll give some examples.
I would be 100% okay with either of the following options and consider them to be "good" in contrast to the other endings, though still retaining the "bittersweet" notion of it all.
- V manages to avoid dying to Soulkiller and was able to stop the neural degradation from the Biochip. This means there is no assimilation, no engram, and no eventual demise for our protagonist, but the original, authentic V we came to care for over the many hours we played as is still alive and well. However, the damage has taken it's toll on our body. We still suffer frequent glitches in our software and vomit blood on the daily. In short: We live, but we walk out with scars to bear.
- V manages to avoid dying to Soulkiller and has discovered the neural degradation can be prevented through a sort of "compatibility." V and Johnny find a way coexist with each other and live in the same body through some modification to the Biochip. It's still in you, but you're not dead. Your body is not wholly your own, but you are no longer dying and can live the rest of your life.