Two story options:
1. Current: More story for the present day, Skullgirl Marie crisis. Story modes for Annie, Umbrella, and (as StarUrania mentions) the other two (probably Marie and Black Dahlia). Could have "what-if" non-canon endings (e.g. "destroy" the Skull Heart or make a wish). I'm hoping for one unified, definitive, storyline. Like, what happens to everyone, who defeats Marie, and how tall of a building does Beowulf suplex Vitale Medici off of? You know, the usual questions.
2. Future: A Skullgirl appears every 7 years. So a true sequel, the REAL Skullgirls 2, should happen seven years in the future in their timeline. So if you want true continuation, look there! Would be weird though. Can you imagine a 20 year old Peacock?