Even though I am currently working on Mojo Jojo right now, I bet that Plankton will win, even with Mojo becoming the giant monster like he did in "The PowerPuff Girls Movie", which I will add in later on, Plankton does have his "Plank-Ton" form from "Sponge Out of Water", but it is just a guess in my opinion.
I actually think Mojo wins for a few reasons, first his job is much harder, defeating the PowerPuff Girls and he succeds much more. Second, Plankton is not as good of a strategist as Mojo. The Plank-Ton has a time limit and it is weaker than the PowerPuff Girls which his robot can hold. And if worse comes to worst he has the RowdyRuff Boys that are the PowerPuff Girls' equals which would destroy Plankton.