I think that was Milligan's run which actually had really good character relationships. Emma could listen to Rogue in a way Xavier never could. She never would've went to him about her sex life and Emma is so casual about things (as one should be). It was a mature take on mutant life without being super dramatic.
There was a video at the time of every editor/writer/etc. saying who they sided with "Xmen or Inhumans" and it was so horribly obvious that it was some PR stunt to push the Inhumans. Emma became like a representation for mutants and what marvel wanted to do to them. Which in a way is flattering, but the execution was meant to be an execution. Did they seriously think people who throw away years of dedication to a franchise for another one because of a half-ass PR push from the company?