I think Trek has always worked well with analogy (so they didn't portray racism against blacks in TOS, they portrayed two races that were half-white and half-black on opposite sides to illustrate the stupidity of racism), and that is what they did (successfully, to my mind) with 'The Host' and 'Rejoined'. They couldn't address the issue directly, so they used metaphor.
But the problem is that you see black men in Star Trek being treated exactly the same as their white colleagues- there is demonstrable, on the ground evidence that in the 24th century, race simply isn't an issue. It doesn't need to be put into metaphor because it's right there in front of you. I think gay characters need this sort of exposure in Trek- they don't need episodes about how they are gay, they just need to be gay and for everyone to be okay with it.