Chopper fighting him makes the most sense, given the past history, and his close relationships with the minks, especially Carrot whom he asked to refer to him as a big brother.
Pedro also basically killed himself to save Chopper and Brook, and the two of them were cursing their weakness after his death.
The Beast Pirates match-ups for the F6 are pretty much already known, so that leaves Chopper with either dealing with the Numbers, or as part of a tag team against Perospero. I'd prefer the later, or being one of those who take out the remaining Numbers, but also getting the fight with Perospero.