It's lightning.

In all seriousness it totally depends on your Roster. There is an optimal choice for a main class depending on which ninjas you have.

Now if we are talking in terms of having all the ninjas... Including the SSN brothers... Then it's lightning / fire with Danzo, Sasuke, Itachi.

Or maybe Lightning with Cursed Hidan, Ay, Danzo.

But if you have stuff like Kazekage Gaara and Sage Naruto, You'd probably say the best class is Wind.