Y'shtola still took up the space that could have gone to literally any more interesting female character that didn't necessarily have to be a researcher. Researchers are boring, and if that's all that's going on then it's going to get old real fast. The fakeouts she's had haven't helped much in the way of soldifying her importance-they have actively cheapened her and made her a joke. Her most interesting moment in Endwalker for me was when she turned us into frogs. Everything else was forgettable.
I'd rather have characters who react in the moment to the world around them like Estinien or Venat who aren't afraid to do their own thing in the middle of an otherwise unreasonable situation. Venat was clearly intelligent, but also a no-nonsense individual who broke herself out of Hermes' spell and went straight after Meteion instead of giving us some long drawn-out speech or a snarky remark. Y'shtola is stagnant-a know it all with no further capacity for growth and who is passive to what's happening in the moment.
The only way someone could tolerate her at this point is if they find her visually appealing, but failing that there is nothing of substance to latch onto anymore. Our next postergirl could easily eclipse her in terms of looks and personality if they ever bother to design one. She has served her purpose, let her exit stage right.