I don't think some of what you're saying makes much sense. You can't literally just reverse most of those stories. A lot about how those stories went is related to the core of Jean and Scott's characters. Scott has always been portrayed as more flawed in a way. That's not a point against Scott. It makes him relatable and human. He and Jean have always been different types of characters. I personally don't find Jean a very relatable character. I can see why she would be for some women, but she has always been presented as more of a character you would admire rather than relate to. The original Jott dynamic was all about Scott being angsty and insecure and Jean trying to break him out of the shell.
Anyway, to one of the reasonable reverse scenarios, that is related to the era I was discussing, the one where Jean/Logan becomes a thing and Scott dies instead and she gets to be a main character on M-Day, Schism and etc(Not AvX, that story doesn't make any sense with her alive). Yes I probably would have liked that. I love the idea of Jean being a leader, the center of the franchise and interacting with the overall MU. Why wouldn't I? That's exactly the reason I don't understand why most Scott fans play victim about it. I guess as someone who prefers oldschool Scott AFAIK it makes sense that you weren't pleased with the direction for him, but that doesn't mean he got screwed over. Those decisions made him the central X-Men character and gained him a legion of fans.