Going with only Torrent as a ability for both.
Greninja is problaby faster, but weaker than Samurott.
Samurott doesn't have alot of variety, but what he lacks in variety, he have in power. His go to STABs moves problaby are Hydro Pump, Razor Shell and Aqua Jet. Hydro Pump is Strong as hell, Razor Shell is a good attack, not his strongest physical STAB, but it has a high chance of lowering Greninja's defense, so that is a good bonus, Aqua Jet as a Priority Move to outspeed Greninja, but Greninja has his own spam Priority move, so Aqua Jet is quite useless here.
His other moves to have in had are good as hell, those being Megahorn, Sacred Sword, Super Power, Slash, Night Slash and Air Slash. Megahorn, Superpower and Sacred Sword will do a massive amount of damage on Greninja, since Samurott has Expert Belt to boost his super effective attacks by 20%, Air Slash for Good range attack, and Slash and Night Slash for Critical hits.
Speaking of those, Focus Energy will also be effective here if he goes with Slash, since that move raises the Critical hit chance. Samurott also has amazing precog via Detect, and Copycat to use a move from Greninja before it or Encore to lock Gren in a bad move. As for Stats, he has Swords Dance to amp his Physical AP, Screech and Tail Whip to lower Greninja's defenses
Now Greninja has alot of moves to cover, his Main STABs are Water Shuriken, Hydro Pump and Night Slash, his other moves are Shadow Sneak, Lick, Extrasensory, Power-Up Punch, Bounce, Quick Attack and Gunk Shot.
Hydro Pump is the same as Samurott, Night Slash has the advantage that it is not resisted by Samurott, besides the Critical hit and Water Shuriken is a good priority move, same with Quick Attack and Shadow Sneak. Lick can paralyze Samurott, same with Bounce, but it needs to wait more for it to happen, Extrasensory can flinch Samurott and Gunk Shot can poison Samurott, all of these are good, but Poison is problaby better IMO, Power-Up Punch is to give Greninja some attack boost.
For Stats, Greninja has Growl, Smokescreen and Double Team, growl will lower Samurott's attack, though Swords Dance will regain that more fast than Greninja can use it, Smokescreen to screw up Samurott's vision and Double Team would be usefull, if Sacred Sword didn't bypassed Evasion stats changes, and while Smokescreen is good, but his own Haze will likely, counter that, mainly for the fact that i don't think that Greninja will let Samurott using Swords Dance.
Spikes and Toxic Spikes will be a good form to do chip damage, but Greninja will need alot of setup for this. Substitute is good, but that won't survive a Megahorn or Sacred Sword. Camouflage can make Greninja lose the Weakness to Sacred Sword and Super Power, but it will give one to Air Slash and Megahorn is still here.
Overall, Samurott take this. His moves do alot of damage thanks to its typing and Expert Belt, with Swords Dance to amp he. Most of Greninja's own Stats Reduction are countered by SD and Sacred Sword, while Smokescreen is a pain in the ass, but likely it will be gone with Haze due to free setup for Swords Dance. The Spikes needs alot of setup and Substitute is likely KOed with a single move, plus, Encore to lock Gren on Substitute or other move that is bad for him and Detect to predict some nasty moves. Samurott Low to Mid-Diff this with only Torrent