You can see the character growth unfold. The themes are a little disconcerting if you're not used to stuff like rape, child prostitution, abuse, etc. but they're handled with care.
http://www.mangago.zone/read-manga/yatamomo/
You can read the prequel but I prefer Deguchi and Onoda's story. This and the prequel are complete.
http://www.mangago.zone/read-manga/soredemo_yasashii_koi_o_suru/
Speaking of Yoneda Kou, you can't say good plot and character development without mentioning this beast!
http://www.mangago.zone/read-manga/saezuru_tori_wa_habatakanai/
For less heavier plots... Simple plot but the well-paced romance makes up for it as well as the character growth between these two as a couple and as individuals.
http://www.mangago.zone/read-manga/blue_sky_complex/
I also prefer this over the prequel. Hoizumi's character development was a spectacle to watch. c:
ttp://www.mangago.zone/read-manga/love_nest_minaduki_yuu/
A glimpse at the gay porn industry. There's just something about this one. Season two's just started as well.
http://www.mangago.zone/read-manga/walk_on_water/
This was nice too. The plot's intriguing.
http://www.mangago.zone/read-manga/wolf_in_the_house/?av=1
For shounen-ai...
http://www.mangago.zone/read-manga/kimi_wa_natsu_no_naka/
http://www.mangago.zone/read-manga/karasugaoka_don_t_be_shy/
http://www.mangago.zone/read-manga/blue_blue_blue/
http://www.mangago.zone/read-manga/koi_wa_kamen_no_uchigawa_ni/
http://www.mangago.zone/read-manga/king_s_maker/
http://www.mangago.zone/read-manga/19_days/
yaoi/shounen ai with good plot and character development?