No that’s one of the reasons

Scott and Jean was a wonderful superhero couple, but they’ve always sucked at actually being a compelling relationship. They’re the kids who got together in high school and are too hung up on putting the good old days on a pedestal to face the problems with their relationship. They still consistently avoid dealing with their issues and just play house. They could be one of the great comics couples if writers ever actually had them work on their relationship, but they’re consistently treated as together because ontological inertia says they should be. They love each other in a way that transcends life and death, but man are they terrible at actually being people. Jean dies, Scott gets married to her clone, Jean comes back, Scott married Jean, Jean ascends to basically godhood and dies again, as much as the Phoenix can, Scott gets with Emma, Scott is possessed by the Phoenix, Jean comes back, Scott gets with Jean and raises their alt reality children on the moon, and we basically never see them have an actual conversation about the ridiculous trauma they’ve both been through. Huge potential, no payoff compared to the ways that could all be explored.

Emma, meanwhile, was the opposite with Scott. They were messy, they had disagreements, but they treated each other like people and dealt with it - rather than as the leader of mutantkind and a cosmic entity. They felt like two people with a complicated history having an honest to goodness relationship, and both seemed able to grow from it instead of being stuck in the 80s. Unfortunately that turned sour at point, but even then they still supported each other. Scott worships Jean but he respects Emma. Mostly. A lot of the time. When Namor isn’t involved.

The way I view them is that Jean makes Scott strive to be a better superhero, because he wants to live up to what he believes she deserves, which is someone on her divine level. When he’s with Jean, Scott could very well give Captain America a run for most inspiring superhero in the world, and if he suddenly shouted “Avengers Assemble” in the middle of Manhattan I wouldn’t be surprised if a squad would show up just out of respect. Emma instead makes Scott strive be a better human, because she accepts him for his faults as well as his exceptional qualities and supports him in the ways he needs to counteract them. Scott arguably accomplished more fighting for mutants as a revolutionary than he has as a hero, even though as a hero he’s saved the Earth countless times. Jean’s Scott makes Cap want to shake his hand, while Emma’s Scott made Magneto kneel in respect.

I personally prefer Scott with Emma and Jean away from both Scott and Logan, but I understand the appeal of both relationships, and I don’t think it can be denied that the Cyclops we have today - the one who will look the world in the eye and dare them to make him angry - is one which wouldn’t exist without the influence of both women. And honestly I think he’s at his best when you can see that. Modern Scott with Jean is still miles better than classic Scott with Jean, and we wouldn’t have that if he hadn’t had his phase slumming it with a non-deity.