All the people in vault 111 died or were killed except the protagonist's family, pretty silly. The Institute needs people who are free from radiation contamination, so what do they do? That's right they kill one of the 3 living members because she wouldn't immediately let go of her infant child....completely stupid. For some reason the writers decided to try to trick the player into thinking that Shaun was 10 years old (why would he make a 10 year synth version of himself...?), and then having him being the leader of the guys who have been trying to kill you the entire game was just wrong. And then, after you kill everyone and everything in the Institute base, you nuke it for no apparent reason. All of that pristine stuff inside could have been used by everyone else in the wasteland but nope it all went boom, AND you kill Shaun in the process because he stayed behind.

Please hire better writers next time...