Not sure why everybody gets hot and bothered by plot lines and their divergence from their own predilections. Very early on, the game's plot deviated from the original 'Hook' and suggested plot elements, I guess mostly for commercial reasons and that is as it should be, if you want to run a team based development with regular updates. This means that plot direction will be heavily influenced by the market. Hey, I didn't like it when Cadbury's was taken over by Kraft and they changed the recipe of Dairy Milk … I eat a different brand now … Niche stuff is expensive to make, especially as few actually put hand in pocket and fund it and it is naïve to expect a game not to change its plot line to follow the biggest revenue stream.
By all means fantasise about future plot developments; but, unless your niche aligns with predominant ones, don't be disappointed if the game does not go in the direction you want it to