I disagree, it's a core aspect of what makes Spider-Man, Spider-Man. I think we're also forgetting that in-universe, Peter Parker is hot. All of the superheroes are hot, unless specifically stated otherwise. Peter being a nerd doesn't make him ugly, just not as stereotypically masculine as someone like Flash, or able to afford to be as well groomed and put together as someone like Harry. It seems less like MJ is a hot trophy for Peter and more like we're just supposed to be taken aback by the type of guy she's going for, not that she's so much more beautiful than him they look physically mismatched. At least to me.
It doesn't matter, that's why I'm not sure why you're framing MJ being hot as a problematic aspect of the character (or her relationship with Peter) that requires analysis. Comics didn't decide to associate models and actresses with physical beauty, society did that. Superhero comics are largely about escapism and idealized depictions of humanity; humans like beauty. There are also versions of the character that don't have her looks played up, MCU MJ for example is never depicted glamorously.
Ok, but I've seen people complain about her not being "hot" in other adaptations.
I guess my point is: why are people so attached to this idea?
Mary-Jane being attractive is part of her lore just like with other characters like Storm, the Storm siblings, Steve rogers, She-Hulk, Thor, etc.
"Cable was right!"