Well the reason Shaun let you out was revenge. I don't know if you saw the dialouge about it, but he said by letting SS out of cryo, it was his chance at revenge for what happened to his mother. Still, you can easily say that the other method of just meeting SS as he came out of cryo would have been easier and more sure, and why not decades ago? Why risk dad getting shot by a random raider?
Still, with the institute you cannot find enough basic information about what is going on to make a judgement, information that could be gained by being able to make real obvious questions to the characters (but which are lacking since F4 conversation system is seriously lacking. Its like Bethesda is thrusting a major moral quandary over the situation and not offering any data to make it. A big guess. Its not very immersive feeling, it actually all feels pretty contrived and forced.
At least BOS are pretty straightforward, but honestly only because you are relying on old information from the previous Fallouts.
Why is the Railroad so fanatical about synths? You never really get a clear answer about that one, it does not match everyone else's basic fight for survival so why does this one group get to be so leet with their agenda?
The problems with the institute situation are extensive and you all have done a great job spelling them out.
We are all standing here mostly confused about what choices to make and its based on bad writing and poor planning on Bethesdas part. Also the intent was to make the choices not black and white, that is something of a Fallout tradition I think, but I feel the previous iterations gave you so much more to work with. As with so many game releases we are probably dealing with a rushed product with major problems.