What are Madara Uchiha's weaknesses?
It does not seem like any of Madara's new abilities have a counter to sound genjutsu, especially when boosted by Senjutsu / Sage mode.  While sound genjutsu and Senjutsu are both very rare, the manga has shown two examples of different techniques of that type being effective against techniques that Madara has recently gained.

The two Sage Toads' sound genjutsu is effective against the Rinnegan.  When Jiraiya had them use it in his battle with Pain, it was able to easily overcome 3 paths of Pain.


   When Kabuto in Snake Sage mode used Tayuya's flute sound genjutsu, he was able to immobilize both Sasuke and more notably, a Susanoo-wielding Edo Tensei Itachi.  The pair were only able to escape by using Sharingan genjutsu on each other.