A lot of that is she's written as a completely different character when she's in other books that are not her own. She's written as the cool superhero with her amazing costume, and then in her own book she's a (mostly) totally apathetic person that you wonder why anyone that isn't her dad would even try to talk to her.
I think the problem comes from the fact that they never expected her to take off so she wasn't really built for the long game. She was just supposed to show up in Spider-Verse as some random alternate Spidey as a fun little nod. As an example, I definitely don't think they'd have had her reveal her ID to her dad in that one-shot if they were really prepping the character for the long term.
Making E-65 Mary Jane so passionate (MJ in general is definitely a very passionate person, no matter what universe) is good from a conflict point of view when contrasted with an apathetic person.
But this mini really is trying to flip the perception of their relationship. I'm curious how comic fans will feel about it once we're on the other side of this story.