I'm sure Madara doesn't have more chakra than Eight Bijuu, and when the user becomes exhausted, the Susano'o loses strength. Gedo Mazou has more chakra and can use more Ninjutsu (we've seen where it used Lightning Release in the anime). The Mazou's strength doesn't rely on the user controlling it, it relies on the chakra within itself. I would say Gedo Mazou wins with great difficulty, but this is quite a hard one. The Perfect Susano'os defensive are expected to be on an entire different level than a regular Susano'o, Gedo Mazou may not be able to break such a defense. I think it all comes down to time, as soon the user of The Perfect Susano'o becomes exhausted, is the more vulnerable he is to attack. This match-up can go either way though, we haven't seen enough of their abilities, especially the Perfect Susano'o.