Madara stomps in S1, S2 depends on the influence of the Rikudo Chakra that Madara obtained when Madara got the Rinnegan.
-Each Rinnegan eye has extremely powerful chakra inside it, Obito wasn't the original user and he couldn't handle one, so just imagine the kind of chakra that those eyes would run through the original user's body once they got them back.
-As Hagoromo stated, when Madara merged Indra and Ashura's chakra, Madara got Hagoromo's chakra, which let him awaken the Rinnegan in the first place, so this should mean that Rinnegan Madara's Susanoo>>>EMS Madara's Susanoo due to far superior chakra.
-Madara also has Senjutsu enhancing his Susanoo.
The main factor is the Rikudo Chakra, and whether or not the chcakra he got from the Rinnegan can be compared to what Kakashi has. Kakashi got his from Obito, who in turn got it from JJ Madara, who got it from the Juubi. Juubi and Rinnegan, two halves of Hagoromo's power. If you can get his chakra from one, you can probably get it from the other. Is the chakra he got the same as what Kakashi got? Is it around the same quantity? Will it have the same effect on PS? If so, Madara wins, if not, Madara doesn't stand a chance. Juubito will still need to get Bijuu Dama off to win.
-Any kind of attack used with the Gudo Dama is useless. The strongest attack delivered with the Gudo Dama as supplements only managed to destroy a Senjutsu Susanoo. Senjutsu PS (Possibly a boost from Rikudo Chakra)>>>>>Senjutsu Susanoo. A small Bijuu Dama cracked the Gudo Dama, Senjutsu PS would cut any Gudo Dama apart.
-Chakra Arms got countered by the Kurama Avatar, Senjutsu PS manhandles them.
-Shinju? Madara evaded that in canon.
There's also the jump between One Eyed JJ Madara to Two Eyed JJ Madara. The same jump applies to One Eyed SM Madara, and Two Eyed SM Madara. Is the Juubi a much better boost than the Rinnegan? (Full power of the owner) Or are they around the same level individually?