Would it be better for farm for Mr.3 in the mission where he has clones or not? Would the increase chances of him dropping?
From what I've read, the odds are about the same on either chapter. However, if you farm on the final chapter, you'll be making (slow) progress towards a new title and an extra friend slot at 50 clears, if that sort of thing matters to you. Chapter 15 is also a more cost-effective cola farm, with better XP, way better Beli, and Daimyo Turtles.
TL;DR, unless you also want to farm for Miss Valentine, I'd just do Chapter 15.