I don't know, I thought her lewd scene in Episode 2 was very hot and quite sweet. It also has one of the few instances where the DIK/CHICK system actually feels like a representation of the MC's personality rather than a game mechanic. A pretty solid win there, IMHO. I agree with others that Maya's problems begin in Episode 4. First, her misleading of the MC is never properly addressed, and second she remains too central a character even if she flat out rejects the MC.
But I disagree about main girls: Maya, Josy, Sage and Jill are all pretty clearly main girls. They have obvious sub-plots, thematic music, spend a lot of time with the MC, and as of Episode 6, Hangouts. The only one who feels extraneous is Bella, who would probably feel like another version of Jade or Cathy without the title cards. Likewise, I think Quinn is the only one of the side girls who might be mistaken for a main character, given how much time, focus, and led content she gets.
I think it's important to remember that the game isn't close to ending yet. The MC can't resolve all the problems with his favorite LI yet, because if then they would be free to live happily ever after and the game would effectively be over. So girls like Jill and Sage* are still peripheral because they need a slower romance to keep pace with the overall story.
I think the reason the Maya and Josy tangle was 'resolved' so early was specifically so that DPC could introduce each character separately, then introduce them as a couple/thruple, then give them a normal helping of relationship-threatening drama. He wanted players to be invested in Maya & Josy as a couple but still see them as individuals, and he thought a surprise tragic love story would be the best way to do that.
The real obstacles to M&J begin now, and it will be up to the player to either keep the trio going/put it back together (if possible) or pursue one of the girls and deal with the fallout to the other. So in that sense, Season 1 is a prologue that sets up M&J. Season 2 will be about the MC actually pursuing his preferred romances in the face of obstacles, and presumably Season 3 will be about removing those obstacles and letting go of unchosen girls.
I do think DPC miscalculated by allowing M&J to remain a central focus of the game after they reject the MC. And he definitely underestimated the amount of work he needed to do in Episode 4 to make up for the way the MC was treated. So the execution was poor. But the basic idea has some potential, IMHO.
*With Sage in particular, I don't think being her fuck buddy is the only way to romance her. So you haven't closed her off as a romance option just yet, you've only closed off one avenue to it. Getting rejected by M&J may be similar, with individual routes opening up again after the break-up in a future Episode.
Yeah, if there's one thing we know about DPC it's that he never tries to trick or mislead us!