http://www.mangago.me/read-manga/let_dai/
there are straight and gay couples.
http://www.mangago.me/read-manga/uragiri_wa_boku_no_namae_wo_shitteiru/ although they r not actually gay (fantasy genre is tricky)
andddd: http://www.mangago.me/read-manga/shimanami_tasogare/ (its not even a yaoi/shounen ai but the mc is gay)
If you're into a heart fluttering yuri where being gay or whatsoever is not an issue, then this one's for you. Enjoy!
http://www.mangago.me/read-manga/yurikon/
Is there any manga with lgbt people but where them being gay or trans isn't the main plot? Like it's just part of the story. Kinda like Banana Fish.