BL that has a lot of focus on the side couple (it's really good, and it's definitely not what it seems like upon first glance): http://www.mangago.zone/read-manga/someone_else_s_bl_manhwa/
BL with an actually healthy relationship and no shitty rapist seme with a bad attitude that takes advantage of or looks down on the uke:
http://www.mangago.zone/read-manga/fools/
http://www.mangago.zone/read-manga/kamisama_to_toberanai_tsukai/
http://www.mangago.zone/read-manga/koimonogatari/
http://www.mangago.zone/read-manga/awairo_emaki/
http://www.mangago.zone/read-manga/heesu_in_class_2/?G6We
http://www.mangago.zone/read-manga/dream_away/
http://www.mangago.zone/read-manga/the_story_about_you_x_me/
http://www.mangago.zone/read-manga/sugar_dog_life/
http://www.mangago.zone/read-manga/inma_kun_wa_oshigoto_dekinai/
http://www.mangago.zone/read-manga/i_seriously_can_t_believe_you/
http://www.mangago.zone/read-manga/whatever_the_start_may_be/
http://www.mangago.zone/read-manga/angel_buddy/
http://www.mangago.zone/read-manga/fate_makes_no_mistakes/?texD (Main couple is the literal definition of respect for both parties, can't say the same for the side couple, but their development is ongoing)
I'm always on the lookout for yaoi/bl with a long storyline that focuses on the main couple but it always ends up either being a few chapters on the main and then side couples or the story feels rushed. Are there any long term (it doesn't have to be completed yet as long as the story has recently been updated) seme isn't a jerk, uke isn't a total weakling (Make the rape stop ;-;) long manga/manwha?