How can it be countered? Look at Madara is doin now he is ownin the kages in its not becuz of his rinnegan or wood that he recieved, it becuz of his sanunoo how did hashirama break thru it when the current kages are struggling?
All of the techniques have a down side and it is usually the amount of chakra to maintain it.
Look at naruto during the current mangas he has been able to fight multiple enemies, couple of em were top ranking hokage, he has used rasenshuriken like a bajilion time (when in sage mode he has like 2-3 uses right) he is uber strogn, able to sense danger, uber fast, he is even kinda smart for some odd reason.
But this comes at a cost. His chakra kakashi even states that sasuke and naruto have large amounts of chakra and too learn sage mode a person needs alot of chakra to be able to balance it out with natural chakra. So naruto has to lose chakra to gain those abilites.
Same goes for EMS and Rennin although the user has a large chakra reserve the most they use require large amounts of chakra even witht he users great chakra control (we dont need to go over chakra control do we?) So everytime they use Ameretsu, Genjutsu, Sasunoo. They take huge hits to their chakra and eventually are unable to fight anymore (we dont neeed to go over what happens when a ninja has no more chakra do we?)
So they get wrecked by over using there eye techniques, Thats more than likely how Hashirama won. He is also a master of water and earth techniques and has uber stamina and stregnth (he is senju).