Disclaimer this is my personal analysis of the situation. Feel free to disagree.
Why has 616 Mary Jane suffered so greatly in the Post-OMD continuity? After much reflection, I think I've discovered the answer. Unlike Spider-Man's other historical love interests MJ simply doesn't have much of a character beyond being a love interest, at least not in the twenty years proceeding OMD. While Gwen suffered from this state, one could plausibly argue even more so than MJ currently does, that has changed in recent years due to the success of Spider-Gwen and the Amazing Spider-Man Film Series. MJ unlike Black Cat or Silver Sable, for example, lacks agency of her own. While they are a thief and a mercenary respectively who do exciting things besides being Peter's bedmate MJ is not. In most media, she appears in she is nothing more than a damsel in distress needing Spider-Man to rescue her at various points in the story or the worried spouse standing helpless, & impotently, by the window awaiting Spide-Man's return. In essence, she consistently is presented as a plot device not a completely realized character with narrative value independent of the hero. Thus, when one takes away the role of Spider-Man love interest from MJ she flounders as she has no other clear role in the narrative. I'm not saying this cannot change, I'm simply saying this is what has held the character back in recent years.