Really then are you saying Shisui (sorry if i spelled wrong) could never use Susano`o because in at least one of his eyes (which were MS) was kotoamatsukami. Also i do not think that Madara switched back to EMS to use Susano`o but i will reread this.
From my understanding:
Itachi can use Susano'o coz he's awakened Amaterasu and Tsukuyomi.
Sasuke can use it coz he has shown to use both Tsukuyomi and Amaterasu which would then give him Susano'o
I'm not very clear with Shisui so correct me if i get anything wrong but, Shisui's eyes were not MS. His ability was something that was unique to him (again please correct me if I'm wrong)
In Madara's case I think because he
awakened Rinnegan he is still able to use his MS powers because he also has MS either that or Kishi made another mistake (similar to Raikage's arm)
And Nagato can't use it coz his Rinnegan was an implant, which means he did not unlock MS, whch means he does not have access to it's powers