Even before being sent to Limbo after the events of Secret Wars, Sue rarely appeared outside of the FF comic. She is way too tethered to the team, even the other members of her team have much more freedom and impact on the MU.
I don't know how Marvel views Sue, but it's nowhere near being the flagship female superhero. All I know is that they should treat the character so much better considering she is Marvel's first lady and deserves a big push.