I'm one of those people who made up Trek series of their own and tried to write fanfic about them. I seized years ago on the idea that the Captain would not be the series' lead, but more like "the chief" character. You know, like the precinct commander/shift commander on a cop drama, the DA or senior partner on a legal drama, the chief of staff in a hospital, you know. They're rarely the lead character, and instead they're the mentor, the voice of wisdom, the one who stays "at base" and keeps everything running. Usually they're a fully fleshed-out character in their own right, and it's not like they're completely separated from the action, but it always struck me as dumb that the captain is the one putting themselves in harm's way for the sake of drama. Picard and Sisko didn't do that as much but even they did so more often than they should.
My general idea was that the show would have an ensemble cast, with the captain played by a recognizable character actor/actress who would be billed at the end of the credits like so: "and So-and-So as Captain Such-and-Such". The captain would not, at all, be a minor character, and in fact would remain prominent, but there would be less of a need to have him or her constantly leading landing parties/away teams just because they're the lead character and thus need to be in the heat of things.
I flirted briefly with the idea that the main cast would be made up of "lower-decks"-type crewmembers, such as a security officer who regularly was part of away missions, or a shuttle pilot, deck department officer, etc. I don't think that would work, though, but keeping the captain as a prominent-yet-supporting character strikes me as a good move.
I also wanted serialized plotting, but in a manner more like Buffy or The X-Files, so that there would be plot threads that continued for the entire season, being the focus of most episodes, but the odd standalone A-plot wouldn't be impossible. I loathe the reset-button, and it seemed like Trek was determined to stick with it at all costs, usually at the cost of character development, and making every episode feel the same. The last two seasons of Enterprise were too little, too late, and while I loved DS9 when it was on, I have issues with that show, as well.
Purely episodic plotting needs to become a thing of the past. It only exists because in the early days of television, there was no such thing as VCR's and even reruns weren't really a thing until the 70's or so. Audiences had to be able to watch the episodes in any order and still have them make sense. But it's not the 60's anymore. And think about it; every other medium we demand serialization. Novel series are usually very self-referential, even if the individual books have stand-alone plots. Movie series are the same way. Why on earth do we demand TV be purely episodic? And really, hardly any TV series these days really is, even those that don't try to be. There really isn't a TV series on television in 2016 at all that uses the reset button. There's a reason for that. The reset button SUCKS. It kills drama, it promotes flat characters and story stagnation. It stifles creativity and makes the show seem pointless and boring.
As for the gay character(s), I agree it's past time for Trek to have them, and it's pretty odd that they had multiple opportunities to explore this idea and refused to take them. Why couldn't Jake and Nog have fallen for each other? Why couldn't Garak have been in love with Bashir?
The only thing I ask is that they be handled the same way characters like Sulu and Uhura were. Here were two actors of color on television in a time when such actors always ended up playing villains or subservient characters, and their color was usually an issue. But here they were equals with the rest of the crew, and they weren't there for tokenism, and their race wasn't made an issue.
A gay character or characters on this show need to be handled with the same kind of grace, subtlety and matter-of-factness as the straight characters would be. No character on Trek has ever made an issue of who they like to sleep with, and for all we know several of the characters might have been bi, but it wasn't talked about or made a big deal. It just happened. So, having a gay male character on this show, who is a fully fleshed-out character with a real personality who also happens to be gay would be just fine. And of course, such a character would be shown to have relationships or at least flings, each of which treated the same way as you would if the character was straight.
What would suck is if the character kept mentioning their sexuality every so often (see the TVTropes entry on "Have I Mentioned I Am Gay?") and/or kept running into alien races that couldn't handle the idea of homosexuality so they can deliver a ham-fisted sermon about gay acceptance. This is 2016. We don't need those sermons anymore. And besides, they're counter-productive, anyway. I've never once heard someone say "I used to be homophobic but then I watched a TV show that told me all the ways I was wrong, so I changed my views", but I have heard, even in this very forum "I used to think homosexuality was gross, until I saw two guys kiss on a TV show, and realized it's not any different." Also, the gay character(s) sex lives should not be any more active than the straight characters. We don't need to see two dudes in bed together all the time in order to let us know they're gay.