Sole game I can think of that actually make use of yuri as a gameplay mechanic is Valkyrie Drive, where kissing the girl partner turns her into a weapon (enabling new movesets and stronger attacks). I recall it also being a better Senran game overall than the SK games too.
Elan Plus is a japanese simulator game where candidates are selected for the Elan project, a plan meant to migrate to a new planet. Conversation choices with characters are a bit deeper than the usual japanese romance simulation game as you get to choose the emotion tied to the responses (sad, angry, happy, normal, etc) which can bear different results. It's possible as a female character to have romantic relationships with the heroines and the same is true in reverse for the male main character
The Atelier Arland trilogy have their fair share of yuri teasing, and Totori is the most known out of the bunch for the Mimi route (which I've heard became canon in Atelier Lulua).
Super Robot Wars T features the three female assistants progressively having the hots for MC and you can choose as female MC to drop the hint in the true ending's epilogue that you don't mind a romantic same-sex relationship. SRW V had the Cross Ange plot, tso hings went awfully gay mid-game with the redhair girl declaring her love to Ange and being reciprocated in return.
Haven't played Mary Skelter 2 but I've heard the two main heroines get to be together.