Without that story or a variant of it the entire game doesn't make sense. Almost every quest looks, from different angles, at the question of what is a soul and what is consciousness. A number of quests look at the duality of the soul. There is a band in the game called the Cartesian Duellists (from Cartesian Dualism -- Descartes' view of the distinction between mind and body). Without the Relic, that doesn't begin to make sense.
I mean, honestly, if you don't have a Silverhand type story what on earth did they do that for???
If the game was intended to be zero to hero (which I think is unlikely but who knows), well, thank God they changed their minds because even by the end of Act 1 Jackie has run out of character traits and there is rather limited scope for any kind of intelligent narrative in that setting.
Questions about soul and consciousness, what's real and false, are generic to the cyberpunk scenario, which right from the beginning offered the possibility of your brain being so diddled by technology that you don't know up from down. What are called "Dolls," "Engrams," "Braindances," "cyberpsychosis," etc., etc., all those tech things that open up the possibllity of a distinction between soul and mere memories - all that stuff, those were all topics mooted as early as the early 80s in the genre fiction and the gee-whizz science books that partly inspired it (for example Douglas Hofstadters
Gödel, Escher, Bach, a very popular dinner table discussion book in the very early 80s), and put into a neat bundle by the developer of the tabletop system.
The game does handle that side of things well - the story "brings it home" in a realistic way - but it's not some special topic that only this particular game, as part of the cyberpunk genre, broaches.
And again, if the game was not intended as "zero to hero", then they wasted a whole lot of time and effort in building a setting for precisely that.
As I say, the compromise resolution may be that they
had intended something like this story - but for the endgame, for the resolution to the story of the character you'd built up in the traditional RPG fashion. As it is, V
has no story (unless you do the RPG content, which then makes a mockery of the urgency of the MQ), and without that, without V having a personality that you as the player care about because you've built it up in your mind through playing him and living with him, there's no actual dilemma between V and Johnny, so the story has little bite and it
is pretty much just Johnny's story.