Janet worked for SHIELD on the super-soldier programme in Ultimates before becoming Wasp.
Carol Danvers is a SHIELD operative in Ultimate Marvel and replaced Fury when he was left in the Supreme Power verse. She's still currently running Ultimate SHIELD
Maria Hill(?) the female SHIELD director from 616 recently.
Betty Ross from the Hulk flicks could appear. (will Liv return?)
there's other female SHIELD agents, including Bobbi Morse aka Mockingbird and Sharon Carter who played a large role in Ultimate Spider-Man...