It would be a tough battle between Sasuke and the Six Paths of Pain. A LOT of the fight between Naruto and Pain played out the way it did because of conditioning: Naruto's Sage Mode caught Pain off guard in the chakra absorbing, Pain underestimated Kurama [Naruto would have lost without Kurama], Naruto's enhanced physical and sensing abilities due to Sage Mode saved him in a few instances, etc.
It'd be very interesting to see how the same fight would play out with Sasuke in Naruto's place, but in the end I think Pain would end up taking the victory. Sasuke has Amaterasu, but Its still not clear how Pain reacts to the flames. This particular debate topic is still hot in the ever-so-classic "Itachi vs Pain" debate, so lets call it a draw on that one for now.
Sasuke has Susanoo, but there is the possibility of Pain being able to absorb Susanoo away from Sasuke. Susanoo is after all chakra manifested, and if Pain could suck the Sage chakra from Naruto, theres credibility in assuming Pain could do the same for Sasuke's Susanoo.
Sasuke has speed, agility, and is an expert swordsman, but Pain is able to keep tabs on him via shared eyesight. Again, Naruto only was able to best Pain in this regards thanks to his Sage Mode fighting style.
Another key factor in Naruto's victory was the use of his summons. The toads played a huge factor as Gamabunta was able to separate the summoning Pain away from the others inside his mouth, allowing Naruto to kill that Pain.