Nothing in this world is truly black and white, but play along with me here.
A protagonist in a yuri anime will either be conscious or not aware of her own sexual orientation. In other words, I’m asking you to understand that I’m simplifying things since I’m considering confusion (about sexual orientation) to be on the same side as being unaware.
With such a reductionist limitation in place, I ask you this: is it better for a yuri anime protagonist to be aware or not?
Unlike in real life, where I would unhesitatingly say it is much better for people to be comfortable and aware, the answer isn’t as clear-cut in yuri anime.
An unaware protagonist means there will eventually be an Eureka moment. Things will click and the character will realize, “I’m gay!” (or bisexual or pansexual or so on). Sometimes it’s flashy and the narrative will put this quest for sexual identity on prominent display. In Flip Flappers, for example, Cocona has to come to terms with her attraction to Papika throughout the entire series and her struggles define episodes 5 and 7.
For those of you who aren’t aware, Cocona and Papika travel to and from Pure Illusion, which represents a part of someone’s psyche or unconscious desire, for most of Flip Flappers. In episode 5, the girls travel to an all-girls boarding school (the classic setting for Class S and yuri anime/manga/visual novels/etc) and in episode 7, Cocona has to sit through and see alternate versions of Papika play the role of romantic interests as commonly seen in anime and manga.
While such depictions are both flashy and entertaining, such moments of realization are usually not like this in other series. The female character, upon realizing her sexual orientation, is apt to deny herself as she, brainwashed by a heteronormative society that condemns relationships that aren’t between man and woman, believes it’s improper for girls to like other girls. She is scared of being wrong. “Girls can’t like other girls” is how it goes.
What’s actually wrong, of course, is rejecting homosexual relationships.
This leaves me to believe that the inclusion of such a trite and overused line is, in poor taste and harmful. Yet to outlaw the phrase (and related variants) with no exception is also to ignore reality. For there are people who are confused about their sexual orientation and seeing characters go through similar struggles may empower them to come to terms with themselves.
If the protagonist is already aware, then a lot of that tension and drama (and politically incorrectness) dissipates. It’s not a bad thing, but then the narrative loses out on the potential message to be had in yuri anime.
After writing all this, I’m still not sure if it’s better for the protagonist to be aware or unaware. Is the trade-off worth it? The probable answer is most likely, “It depends.” Sorry for the cop-out.