1

Itachi has mentioned in his fight with Kabuto that every jutsu has a weakness, I'm curious as to know what the teleportation jutsu's weaknesses are. Minato seemed to be able to spam the jutsu constantly with no perceivable side-effects.

A possible weakness could be that the user can only teleport to something that has been marked, but there has been no indication that there are any limits to the amount of jutsu formulas Minato could make and also when something has been marked it stays marked forever.

The only real perceived weakness is that it is a jutsu that takes a Hokage level shinobi to master, it does seem to have one hell of a learning curve.

2

Over-reliance and Predictable

If the opponent knows that Hiraishin no Jutsu allows the user to teleport to marked kunai and area, it would be "easily" countered.

  • Minato vs Raikage: if Raikage also knew that Minato left his mark on Bee, he (Raikage) could instantly move to Bee (at this point Raikage already spotted almost all of Minato's kunai) and Minato would probably moved to other kunai and Raikage would chase him again (idk what the final outcome would be though)
  • Tobirama vs Madara: Madara immediately countered Tobirama the moment he used Hiraishingiri because Madara had seen that move before

Of course this can happen (Hiraishin being countered) only if the user of this jutsu rely on it too much and can't finish his/her opponent immediately.

Edit: oh and also if the opponent is fast physically or reactively

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