You completely misunderstood itachis statement he did not mean there was a literal counter for each justu.
But,no justu itself is superior to all other justu and makes you invincible.
1:Byakugou: You can't psychically harm a user under the effects of the strength of a hundred men justu.
But,there are other options.
A.Use funinjustu to seal them.
B.Use genjustu to paralyze them.
C.Tobirama's scheme involving a continuous chain of explosions would eventually have tsunade run out of chakra.
2:Jinton
A.Cab be absorbed since it is ninjustu.
B.Use a ninjustu that has a wider destructive radius.The jinton has so far been shown to take up a immediate and finite space (There mass is breaks down is always in the form of some shape or follows a linear path)
The key to not being killed by jinton is not by countering it with another justu its about analyzing its limitations.
C.Dodge it (Albeit only fast moving people use this option,though an option nonetheless.
3:Susano'o
A.We have already seen people cut into it with fuuton,
B:mess up concentrations of the users by using genjustu
C:and have seen people take advantage of the opening under the base of people's feet.
D:Not mention Mei melted it with her acid.
4:Bijuu Dama
Once again its not about having a justu collided head first with it although,that can be done.
A.Use another bijuu dama to cancel it out
2.Sasukes suusanoo arrow changed its course.
5:FTG
FTG is a very powerful justu and is almost impossible to get around.
However,if you have a constant defense that acts on its own accord you can manage to fend the user off.
Suusano if its up will make sure the user can't get at you
A predetermined explosion would have the user going out with the opponent once they arrive to your position.
You can cover the entire area instead of just near you so they can't FTG the threat away.
If you cant be killed by psychical attacks (Tsunade,oro,juubito,DSM Kabuto,Edos) Use that moment after he attacks you to strike back.
Or if you have an outward expanding/propelling justu use it when you see minato fling a kunai
A.K.A. Needle jizo or spread a katon ninjustu around you in a ring formation/sphere formation.
basically obstruct his path instead about worrying to hit him directly since that won't be an option.
Use poison cloud that only you can breath in so he won't even try to come over
users who can do this are oro,hanzo and mei can spray her acid around herself.
There is a way around any justu.