There are many ways to beat Minato.
1. Magnet release. You can gather all nearby kunais, he will be left with only one kunai jump point. He can ofc still escape to his home, but that is the same as losing. Leaving battle = lose.
He can set marks manually with his hands, but then he needs to move manually away from it, before it's useful. So Minato vs 3rd kazekage (for instance), would be fatal for him, and he would most likely lose.
Just 1 example..
Another is to simply alter the entire battlefield. For instance with lava or amaterasu. This would also remove all marks and kunais. Thus he has only the possibility of leaving battle.
Another thing is to simply gather or absorb every kunai. Obito could do that. Madara or Hashirama could as well, using mokuton. Kitsuchi could use his sand jutsu, to smash the entire battlefield together. Minato can probably escape that by tossing kunai outside of the range, but then again, we don't know the full scale for this. Just making examples.
Genjutsu can also harm him pretty badly, though he'd probably need some extreme master mind in genjutsu, before it would be effective.
Deidaras nano bombs would also be fatal to him.
The battle field could be covered in a mist or dust, bugs, darkness, light, whatever. Blocking his vision would be a great way to fight him as well, making jumps very risky. Minato has shown no sensory abilities, nor has he shown any good smell or whatever, so we can't know, if he can navigate in such situation, though it is only likely that he can, judging from his fearsome reputation. But not knowing it, is the same as saying he can't, till we are told otherwise.
