I finally beat Fallout 4 over the weekend, and this is pretty much exactly how I feel. I sided with the Railroad for almost all of the game, and then at the last minute swerved to the Institute… all the while feeling like every choice I made was foul. I changed my mind mostly because the Railroad decided to act in the same absurdly brutish way as the Institute, which caused me give up on the whole thing and start shooting them because they were closest. I mean, the game was telling me that I had to kill one or the other to proceed, right?
In the end, I felt like taking a shower. Fallout 4 let me down.