Well, for what it's worth, I gather that the main source of resistance to LGBT inclusion in Trek was Rick Berman, and he no longer has any involvement with the franchise. Maybe future movies will be more inclusive (Abrams has said he's open to the idea and is "shocked" that Star Trek has never included a canonical gay or lesbian character), or maybe the next Trek TV series will include a gay/lesbian/bi regular. (Considering that two of the top people campaigning to make the next Trek series are Bryan Singer and Bryan Fuller, that might well happen.)
I'm trying to remember if we've seen LGBT characters in J.J. Abrams's TV series or films to date. I think one of the supporting cast members in Undercovers (someone at the protagonists' catering business, maybe the lead chef) was gay, and there was a recurring thread about catering a wedding that happened to be same-sex. A web search tells me that one of the regulars on Felicity was gay and got married during the series, and another regular had a gay brother who appeared twice. Apparently there was only one recurring gay character in Lost. I can't recall any major LGBT characters from Fringe, Person of Interest, or Alcatraz.