Are there any good otome VNs with a lady protagonist that aren't "pick your boyfriend" or focused on het relationships?
Fatal 12 might be what you're looking for.
I haven't beaten it yet but I'm almost at the end and I've really enjoyed my time with it. It's not really a romance as the game's primarily about the protagonist (Rinka) and her experience being thrust into a game of fate with 11 other strangers (well,
mostly strangers). But she does have a potential romance with another female character that's important to the plot, and the game's most bad-ass character (Odette) is also openly bi. Odette might have the only dodgy character design out of the cast, but given her character and the kind of personality she is, she owns it and it doesn't feel out of place on her.
At this time in the game, my biggest criticism involves Rinka's romantic interest (Miharu) and how much of her plot and her motivations are influenced by Rinka. Like, if it was a het pairing, it would have probably annoyed me a lot more. But I guess the novelty of it happening between a same-sex pairing made it more bearable, and Miharu still has some cool moments. Also, the typical obnoxious anime tropes and gags are extremely minimal. There are a handful, but I'm pretty sensitive to that bullshit and none of it got under my skin.
Let me know if you check it out!
P.S: This isn't an otome game in the slightest, so bare that in mind.