I remember Atelier Iris 2 having a lot of serious yuri not subtext. Like an enemy general who doesn't attack but repeatedly helps you because her "childhood friend" has become one of your party members; a yandere stylist who, when spotting a girl she considers beautiful, tends to go crazy & give her an involuntary makeover; & an alchemist who needs to recruit a harem of mainly beautiful female spirits in order to use her skills properly (the game had 17 elements).