Hirsch fucked up. Plain and simple.
Dipper's crush on Wendy was one-sided and always doomed to fail. It wasn't evil or malicious or toxic, crushes like that are a part of growing up, but when you put a person on a pedestal that, realistically, will never return those feelings the same way, it can only end one way.
While Dipper put Wendy on a pedestal and worshipped his shallow, one-sided perception of her as this hot, cool older girl, Dipper never put Pacifica on a pedestal. He never worshipped her. He started out hating her, and even when he came around, it was because she earned his respect and he came to understand who she was as a person.
Pacifica, likewise, was forced to grow and change because Dipper was someone who wouldn't bend over for her and her parents' wealth.
I don't ship. I don't really get shipping. I hate the word. But if such a huge part of Gravity Falls was Dipper having this crush on Wendy, being hurt but eventually growing up and moving on, then something with Pacifica could have really encapsulated that growth and shown the better, healthier alternative.
But Hirsch is just bad at writing women characters, I think. Pacifica's development seems more and more like a happy accident.