Yeah. I've been toying around with ideas for random elements in gameplay (sorta inspired by how the Blade Runner game did it) for Fallout 4. The whole "who's a synth" thing kinda lends itself to this. I was thinking about a background figure working against the player character throughout the storyline, then to be revealed to be a synth (?) of the player character. Except that it's randomized at the start of the game wether the player is the actual synth, or the other character is the synth. The only way to find out is to kill this other character and finding the synth component (or not). Depending on the faction you chose to side with, this maybe-synth choses a different one and works to further their goals. This would require the questlines to be more non-linear so that the player and the not-player can fullfill quests for their respective factions out of sequence.It sounds like an experimental game that plays around stereotypes and goes meta. Could be interesting once but as you said, I think it would get stale after the first run. It kinda reminds me of Doki Doki Literature Club, once the meta-twist has been revealed, you can't really go back except to unlock additional scenes.
Subversion for subversion's sake rarely pays off.
This way the game would potentially play out differently each time, and play more with the whole "free will" and "how human are synths really" angle.
Anyway, the whole story of New Vegas revolves around this fragile stalemate of all the factions. It's a very important plot point throughout the game (and the DLCs) that the choices of one matter and can have huge impact. It'd overthrow the entire game if there'd be some sort of immutable random ending.