Let's say we don't rule out the possibility that Naruto used the Flying Thunder God technique (which of course, he didn't). What counters is Sasuke going to have to Naruto's extraordinary new powers? It's just like the battle between Minato and Madara. Madara's space-time technique, battle experience, weapons (Nine-Tails) were all superior (not to mention eye techniques), but Minato took him down in two blows. I think many will agree that the battle was disappointing to say the least. Not to go back to the matter of Minato vs. Madara, not knowing whether Kishimoto was rushed to move on to better things, or he simply decided to have the Uchiha, who are regarded as the best of Konoha, lose once (and fairly easily at that), but it seems as if we'll see a repeat of Naruto and Sasuke's battle just like the one that took place sixteen years ago.
Naruto's strength will overwhelm Sasuke, and he will end up the same way Madara did after Hashirama defeated him. Whatever power boosts Sasuke will gain at this point, it really will be no match for the things Naruto has gotten; taking the Rasengan to an entirely newer level than previously, gaining full control of the Nine-Tails' enormous chakra, improving Sage Mode, and not to mention incredible speed. The Flying Thunder God technique will be the last nail in the coffin for Sasuke. Not even Hashirama (similar to Naruto) had such speed when fighting Madara (similar to Sasuke). I am ruling out the possibility simply because it will make Naruto too powerful for the likes of anyone to handle. What weak spot will he have? What amazing technique will Sasuke develop to expose the weak spots in Naruto's powers?
Sasuke won't have the Nine-Tails on his side, so it will be the loss of a weapon which Madara had on his side when fighting Hashirama, and still lost. Madara had the Nine-Tailed Fox again when attacking Konoha, and both won and lost at the same time (he did not destroy Konoha, was defeated by Minato in their one-on-one battle, but did force Minato to sacrifice himself to deal with the Nine-Tails, and killed off a good portion of the village's ninja, using the same weapon Minato died to seal into his son).
Having said all this, what will Sasuke do when facing Naruto? I understand they will be equals by the time they meet, but what good will Sasuke's Eternal Mangekyou Sharingan be if it can't keep up with Naruto's speed (as noted during the Raikage's fight with Sasuke)? Hopefully the circumstances behind Sasuke's new eyes will balance out the power scale between these fated rivals. But until then, I'm going to have to say it wasn't the Flying Thunder God technique Naruto used in chapter 505 simply for the reasons I stated in my post above. Coupled with the fact that Naruto might become much too powerful for anyone in the ninja world. Which I'm sure at least some agree.