I would say that she was already angry and kinda unlikeable in the first game aswell, but if there is one videogame protagonist that has ancexcuse for all of that, is the poor aloy.
People just writing her off as bitchy without understanding all the circumstances around her was pretty moronic.
Yes, she can be a brash bitch, she is also the only one who can do specific things so she has the whole weight of the planet on her shoulders, none of the other "likeable" sony protagonists comes remotely close to her situation, she is not gonna say stupid ass jokes like nate and it would be absurd if she was just an easy going chick.
Not every protagonist must be a marvel character with quips and shit.