Surprisingly, I actually thought something similar, darquegk. The whole incest concept was very tangible so it surprises me that some here did not recognize it, so I question if they even saw the show in NY. The concept of JJ actually being Susan's father, or even the result of incest herself (JJ and his mother) makes a very strong case why JJ wants to keep her under his thumb so much (to protect the secret). Well, that and being a f*cg ego-maniacal monster. The whole reason "For Susan" is such an at-first sweet, then slinky, then skeevy sounding song is because of the subtext with JJ/Susan (he made her his sister, then his daughter... now his wife?), made very clear in the increasingly discordant and skittish orchestration of the song/scene.
As Ethan Mordden points out in his book, this show was just too rich a meal for many. I'm so glad I saw it twice and have my memories because shows like this are very, very rare these days. Particularly shows this audacious with scores this good.
P