Specifically, a manga that develops an LGBT relationship as one of the main relationships, without that relationship being the main selling point like in most shounen ai or yaoi stories. Like a fantasy or crime series that focuses on the plot, slowly develops subtext between two characters, then they end up together. No queerbaiting type titles that hint at a relationship, but then never follow through with it.

Silver Diamond is an okay example, but you could tell from the beginning that they would end up together and that their relationship was a big part of the appeal. But it had an interesting fantasy plot that was the main focus of the story.

Another example would be Lookism, if Daniel and Jay actually ended up together. Something that takes time to develop and hint at the relationship while the main plot is happening. I can't think of a yuri/trans example, but anything like that would be good too!

I've just seen a lot of manga that will tease with gay/LGBT subtext, but then never fulfill the subtext (or even worse, ignore the subtext and have the character get into a way less developed heterosexual relationship).

Ideally, the main plot would be something sci fi/fantasy, or otherwise gripping. Not slice of life. I hope I'm explaining what I'm looking for correctly! Thanks!

Both of these are great, some of my favorites:
No. 6 - scifi
Golden Days - historical time travel/mystery

If you want to read GL, these might also be good:
Paros no Ken - fantasy
Murasakiiro no Qualia - scifi

None of these really have truly happy endings (a bit bittersweet), but the relationships are reciprocated.

Shimanami Tasogare
Well, this actually doesn't really fit into some of the main categories that you're asking for (sci-fi/fantasy that develops into a LGBT as one of its main couples), but it does have many LGBT characters and at the moment, has briefly touched their own backgrounds and stories. I liked it a lot, so that's why I'm recommending it, even though it's still kind of within the limits of what you're asking for.

Jinjuu Houretsuden, perhaps. Still, it's very much like SD as regards to the 'appeal' component. I suppose you've already read Koori no Mamono no Monogatari by the mangaka of SD?

I thought the BL in Umi no Mieru Yane and Hanakisou were very nice and low-key, but YMMV. They both had plot extraneous to the romance, at any rate.

Also maybe Saiyaku wa Boku o Suki Sugiru, but again, it's aiming for the BL fanbase pretty overtly.

Sankaku Mado no Sotogawa wa Yoru looks promising. It hasn't been scanlated, but it is licensed.

I second Golden Days, but only if you're okay with tragic endings. And while plot-wise No. 6 (Novel), which was the original source, is vastly superior to the manga and the anime, it's also not as obvious on the relationship front. I really don't recommend the anime, though: too much content-skipping.

I dunno about Murasakiiro no Qualia. It's very good on the plot front, especially for GL, but the entirety of the plot is romantically motivated much in the manner of Stein's;Gate -- it's in no way something where the romance just happens. But if you do like it, then I also recommend Happy Sugar Life, which is somewhat similar in that regard: weird premise involving a heroine driven by her love for the other girl and nothing else, but still plenty of plot.