Yes I know most people donīt do it but super heros are not supposed to be most people, they are supposed to care for their actions at an ethical level, specially when it comes to the people they love, I personally would have respected his decision to leave Jean, if he truly didnīt see a way out for their marital problems given Jean insisted in exploring her new habilities and after a while start a relationship with Emma than him trying to convince Jean his relationship with Emma was "no real" because "it was just thoughts" this made him seen a flaky character who would change his relationships on a whim and then not confront his own responsibility on the matter.
But then again I also disliked to see Jean blame Emma alone and later I disliked Morrison suggesting Jean putting them together because she could not stop dying around Scott and Emma was better for him but well those are just some of my personal reasons for disliking his run in general
I just didnīt see him as this strong leader Morrison wanted to paint him as, I actually liked more Whedon and later Fraction take on him and Emma than Morrison take.