LAst time i checked susano was a ms tech awakened but unlocking both powers of both ms, rinnegan dont have susano as angato wld have used it as a defence again the Itachi's sowrd of tosuka.
THE REASON RINNEGAN WAS ACTIVATED IN PERFECT SUSANO MODE: Madara said he will respond with his full power, so it means he is gona go full steam which in turn means he is gona use all his abilities to their fullest extent. So naturally he is gona use rinnegan not EMS as EMS<Rinnegan (Proof: u always evolve to something better, EMS--->RINNEGAN but never lose ur base inheritance)
MADARA supposed to have mastered all sharingan powers and learnt all its secrets and thus was able to evolve to rinnegan. So doesnt it in a way imply that he perfected Susano before his rinne or senzu dana boost?
AND yes he can use rinnegan and susano both simultaneously or how else did he call the meteor with a susano? See:
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ALSO wootan are u blind? madara used two chibaku tensei (or similar) to summon the meteors and also used the chakra absorbtion path,
See:
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But i also kinda agree with the fact that rinnegan may have unique abilities per user in addition to its base powers. Plus nagato used chakra rods only bcos his own body was kinda disabled, so he adapted in that way.
ALSO anbukakashi 23 nice observation, but if i may say it: did the fact nagato being a uzumaki matter in this case (he sould have dormant dna of sage)? cos i really dont trust tobi he's a big lier.