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.