Create multiple characters or multiple save points on 1 character and play all of the different quest lines. They're all very good.
If you only want to do 1, I would say to side with the Minutemen and go against the institute.
[spoiler]its far more challenging and a much bigger fight. You first have to defend the castle against an attack by the institute, and then you attack the institute.[/spoiler]
English
-
[spoiler]If you're enemies with the BoS, you then launch an artillery strike against the Prydwen, and have to defend the Castle against a bunch of vertibirds and BoS knights. Pretty epic.[/spoiler]