Dont forget naruto clever at using shadow clones as deception and he also plenty of types of rasengan
yes, but Raiton is fast and casted instantly, wile rasengan/rasenshuriken needs a shadow clone and some time to be casted... By the time he starts trying to make a raseshuriken, he will already be impaled... Also, regular rasengans would not work, as they need to be close range, and there is no way Naruto would make it safelly to close range with Sasuke as an opponet...
With thunderstorm, he would destroy every clone that is close to him, and then, he would only need to cast Senbon all the way around, till he finds the right one... The time would be insufisient to create a rasenshuriken, and rasengan could never hit, as it would ender thunderstorm's area...
You have to calculate the speed factor too, not only the jutsu itself... U_U