For whatever reason, Marvel’s MO with Spider-Man ever since One More Day has been to make Peter as miserable as possible, in an attempt to “call back to how he was in the good ol’ days.” He went from being a (relatively) happy married man, to an aged-up version of how he was at the beginning. He lost his job, he lost his wife, and he even lost his unborn child, all because of an executive who was blinded by nostalgia. And the run that immediately followed this (cough cough DAN SLOTT) didn’t do much to alleviate the backlash.
It looked like they were FINALLY getting over this in the Nick Spencer run. Sure, it wasn’t perfect (the mystery surrounding the new main villain went on for far longer than it should have), but it was a step in the right direction. And then immediately after this, we get a new writer on board who undoes everything, putting him back to where he was after One More Day.
The problem isn’t that “Oh No, My OtP iS rUiNeD,” the problem is that executives are continuously forcing retcons or backpeddling on things like Peter and MJ being a couple, just to make the comic conform to how they want it.
Comparing that with a crack-ship like Hunter and Elmyra, which wasn’t anything that the creator ever had in mind, is like comparing a pizza to an orange.