The easiest way to counter kakuzu eg with breaktroughs, if you are faster, is to use a shark bomb team.

By being slower a good team is: sasuke rs + gakido + ningendo + lightning main or earth main.

Both ningendo and gakido requires full sb and ningendo requires mystery skill trial while Gakido requires chase skill trial.

The idea is that the 1st standard attack chaoses him thanks to sasuke passive and ningendo mystery effects while your team gets a decent boost to defensive stats + shields. After that sasuke will break his immunity to chases.