Nagato wins this
-Nagato uses ST to blow away all the kunais the Minato places,, thus making his use of FTG more difficult,,
-Multiple Summons along with Asura missiles will cover up the AOE of Minatos FTG thus covering the limits of FTG,, seeing as Minato has no prep time at all in this battle,,, to place markings further away,,,
-Nagato being a sensor along with his near instant ST would prevent him from getting blitzed too,, as Minato is not blitzing him without having a mark on Nagato,,, since the latter is one of the best sensors in the manga
-CQC is more dangerous for Minato due to Human, Asura and Chakra rods,,,as the asura armor tanks all the kunai based attacks from Minato,, and his ninjutsu is also absorbed
-Preta counters all of his rasengans,, rather easily,, and even if we take SM into account,, it makes no difference at all seeing as how it takes too long for Minato to knead the chakra,, and preta absorbed 2 SM FRS which are much stronger than that,,
-NO sensor has shown the ability to detect ST,, not only that but the attack is near instant,, the only thing is that the stronger ones required charge up time,,, Minato even after having info on Devas abilities simply cant afford to get near Nagato,,,
-A normal ST from Immobile Nagato destroyed a forest,, a boss sized at point blank range would cover the necessary AOE to damage Minato,,,,Nagato can use Chameleons invisibility along with birds to fly or cerebrus which would also be a total pain for Minato,,,
-Nagato can also use GM soul dragon which minato has to avoid,,,
Minato also has no counters to CT at all,,, as his markings are getting sucked up and he wont be able to teleport something with an attractive force of this magnitude,,, since its not a thrown projectile,, thus nullifying S/T barrier
-Minato needs BM to beat him