I just ran across THIS
article from a year ago. In it, JJ Abrams briefly discusses ideas for Into Darkness
that didn't make it:
“But when you have a movie that’s two hours long, and a group of over half a dozen critical characters demanding attention, it’s hard to find time for all the nuances you want. There was [an idea] implying the sexuality of one of the characters, a back story for another character that was pretty intense, a really funny story we wanted to do with yet another. Hopefully, if there are future films, those other stories will get their moment.”
Sounds fascinating. I hope this stuff is built upon in the next movie.