The concept of sequels in AVNs is always an interesting - but thorny subject - and for a good reason: giving the players various (drastic) ways in which they can play the first game, but then completely ignoring said choices in the sequels is... certainly a brave choice. I can't imagine why you, as a developer, would bother with creating these alternate realities if only one is going to be acknowledged for future reference? Seems wiser to 'slim' down these variables from the start, and focus on updating the game faster over managing all these branching paths that will inevitably lead to a "dead end", so to speak.
And while ambitious, this trilogy sounds like a mountain of work that only a few of us will ever want or see in their lifetimes, but that sounds like a future you problem, so I won't comment on that in detail.
Especially when I look at your "model" AVNs you were inspired by... all of them in development cycles of 1 - 2 updates per year.
I wish you the very best of fortune on your journey, but as of this moment, these are mere words on paper, hanging too close to the fireplace...