If you know Shuriken Shadow Clone Technique:
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That isn't really a counter at all. FTG isn't supposed to just be a direct hit with the kunai. Sure sometimes Minato uses it that way, but it is more so that he can have the ability to teleport across the battlefield at will.
Read the A & Bee vs. Minato fight again. Minato spread his kunai around in random places so that he can teleport to dodge attacks and set up attacks.
He chose to throw his kunai directly at Tobi so as to make Tobi have to go intangible, as their battle was one of speed.
There aren't really any real ways to counter FTG right now except possibly being as fast as BM Naruto, which even then doesn't guarantee a counter to FTG.
be ultra tough in defence like sandaime raikage or sasuke. thats a perfect counter.
If he throws the Kunai towards the target the shuriken hit it away from the target. In a fight where Minato doesn't have preparation and the opponent has knowledge of FTG (When he uses it once his secret is out) he won't just have Kunai lying about. The end.
Weegee. His stare will just kill Minato faster than he can breathe.
I just realized Sasuke's Amaterasu Shield is a good counter before Mark.
I wouldn't say that is a counter, more just a solid defense.
A counter is something that turns around an attack, or builds off someone else's attack to strike back.
To counter FTG well you have to have a solid defense so that his quick movements and strikes wouldn't be able to get you, and you have to prevent him from being able to dodge, as FTG is not just an offensive jutsu.
WS is a good counter to FTG because it can change the battlefield and you can move Marks that are placed
Speed is a good counter because if they teleport to you and you can move fast enough you can hit them right after the get to you
I don't think people understand what a counter is in terms of fighting. Powering through something like the third raikage would doesn't make that a counter. A counter to FTG woud be something like using earth release to put Minato's kunai underground, or the third kazekage's magnetism release to move his kunai wherever he wants.
Even that though isn't a counter if he gets his FTG mark on you. As far as I am aware there is no counter to that, as he can teleport to you at any time from then on out. That means he could fight for a while and then when you least expect it he would teleport to you and kill you.
So my answer is, there are a few counters to his usage of FTG through a kunai. Not many but I gave some examples above. There are no counters though once he has his mark on you.
Genjutsu is the perfect counter to FTG, especially if it involves looking directly into the persons eyes. Hold it.
Why would genjutsu through eye contact be the perfect counter for FTG?
I can see why genjutsu would be troubling but we don't know how regular genjutsu would affect Minato, as he doesn't need hand signs to teleport. He just decides where to go and then does it. Keeping that in mind I don't see why a genjutsu would not allow him to just teleport to a safe location.
Obviously Itachi's Tsukuyomi would be unbreakable for Minato, but people still move in regular genjutsu, it is just that they are seeing things that aren't there. (Deidara, Orochimaru, etc. They were both moving/ or trying to get out of the genjutsu. Deidara even used a jutsu during the genjutsu, which happened in the real world)
So my point is we don't know if genjutsu means he can't use FTG or not.