I think Maya's plot has been a good one, especially for a coming of age story like BaDIK. But I do think it's been hurt by a few structural issues with the way DPC presented it.
The biggest problem is just overexposure. The relationship between Maya, the MC and Josy was the major subplot of Season 1, completely dominating the final episode; the other girls got great scenes, but the focus was always on Maya and Josy. When the situation is finally resolved one way or the other, we have a single (short) episode to breathe before we jump right back into the Maya drama, first with her worrying over the Scavenger Hunt, then in full-on crisis mode thanks to her father.
That's a lot of focus on squarely Maya, particularly since Josy was MIA for the first half and is dragged into the second half
through Maya. Even for a hardcore Maya fan like me, it's a bit exhausting. For anyone less invested, I'm sure it's beyond frustrating by now. We really needed more time to give Maya a turn as a supporting character in the other girls' stories in season 2, the way Jill, Bella and Sage got to help the MC through the "Maya issue" in Episode 4.
Instead, Josy's main drama continues to be her relationship with Maya, Jill gets that interminable blackmail subplot, Bella spends most of her time foreshadowing her marriage issue, and Sage winds up being drawn into Maya's plot directly! Good grief! The only other girl who comes close to getting that much attention is Quinn - and what a shock, she's plenty polarizing in her own right! (Also, a lot of Quinn's screen time is in cutscenes, which makes it a bit less intense since the MC isn't constantly reacting to her.)
On top of that, Maya will always pay the price of memorably demanding 100% honesty from the player, only to keep a pretty fucking big secret from him. I think we can all intellectually understand why she did it, but that doesn't mean it's easy to forgive her for it. I certainly can't blame people who would be reluctant to trust her after that... yet the plot proceeds as if trusting her was a foregone conclusion. Again, this would have been a lesser problem if it happened in Season 3 after we'd switched the focus to someone else. That would have given us time to build up the trust the story really relies on. Instead it just exacerbates the problem of overexposure.
Lastly, we get the infamous library scene at the end of Episode 4. Normally I'd let Bacchus rail against this, but since he's no longer here I guess I'll have to cover it. The problem is that we spent an entire episode watching the MC freak out over the fact that Maya and Josy were secretly girlfriends. He talks at great length about how difficult it was to be lied to and kept in the dark like that. All the while, the MC spends no time whatsoever trying to learn about just what the hell happened between them, or really shows much interest in their relationship at all. Yet when we get to the finale, it's all about how Maya and Josy still love each other, and the MC's place in their relationship is a literal afterthought. Even worse, if the girls reject the MC (for very poorly explained reasons in game), we get that infamous shot of the two making out as the MC walks away.
Just... wow. I mean, I'm as big a fan of the pair it gets
(though perhaps not quite as a big a fan of Josy as ChipLecsap 
), but even I felt the chill there. What we needed was to restructure the episode so the MC spends less time moping and more time learning why things played out the way they did. That way when the finale comes around, the MC can either choose to forgive them and help them rekindle their relationship, or admit he really did care about both and try for something more.
By making the MC the driving force behind the reconciliation on the friendship route, we might at least get a little buy-in from the people who don't want anything more to do with the pair. And by eliminating the rejection path we can avoid upstaging the MC's in his own story. It's still not perfect, but it would have dodged some of the most glaring pitfalls.
But hindsight is always 20/20, and we're stuck with what we got. I think Maya's hatred will probably mellow out a bit if she ever sorts out her problems and finally gets to take a supporting role for a while, but there will always be people bitter about the way she was handled. I'm okay with that. It means less competition for me.
