She needs a decent rogues gallery. She shares a lot of foes with the X-Men, but not too many personal rivalries that she hasn't become buddy-buddy with (and a lot of the general X-Men foes have also become heroes anyways. Magneto, Juggernaut, etc.)
Her Omega status mutant powers are also pretty nebulous. If she was just "controls Earth weather," it would be fine (tosses lighting bolts, can make it rain, snow etc.) But then they go and give her cosmic powers so she can control solar winds and storms, electromagnetic fields, control the air in people's lungs, breathe underwater, etc. She also has the potential to wield magic because, why not? She's simply too powerful to be challenged by most of the popular Marvel villains (Doc Ock, Sabertooth, Red Skull, Kingpin, etc.) So that just leaves cosmic level villains, and how many times has Silver Surfer been cancelled now?