Signs are good so far.
I certainly think Bethesda wants to do better than Fallout 3 or Skyrim (where they had to drop a lot of the planned elements of the civil war before release).
I certainly think it won't be black and white or a choice made for us.
Just look at the synth issue.
You have the Railroad and the Institute with opposing views on synths being sentient creatures with rights.
Then there is the MWBoS which has deep and painful memories of having to fight a robot army.
The idea of synths being mass produced would rightfully be of deep concern to them (or any of the Brotherhood chapters).
Then there could be some rogue mastermind trying to create a synth army for the greater good of course.
How do you deal with that and then how do you prevent it from happening in the future?