Nobody needed to tell us about Bayo. It was simply known.
But in all seriousness, I'm not going to speculate because I
can't speculate because my money's on it being a new IP. Although I think Skullgirls and Shantae could reasonably crossover, LZ just worked on Skullgirls for the past 3-5 years straight, and we already know a new Shantae's in the works, and that it was developed concurrently with the last one. Plus, since LZ's pretty new, their only series is Skullgirls despite their intent to make other games, and outside of Shantae and the Mighty series, WF mostly just does games licensed for other companies. I could see both companies looking to work on something fresh.
Of course, I could be all wrong and this ends up being a LIT sequel.