Itachi-san.
Not sure how Nagato would interact with Tsukuyomi. While he does have the Rinnegan, he lacks the bloodline and has no access to the Sharingan's abilities Madara's Rinnegan evolved from. Tsukuyomi would mean instant defeat with a single eye contact. The shared vision would potentially make it even worse, because as soon as Nagato looked into Itachi's eyes through one of Pain's or the animals eyes, the Genjutsu would unfold its effect, trapping Nagato's psyche within Tsukuyomi.
Amaterasu on the other hand could be able to effectively deal with Chibaku Tensei, by aiming it directly at the sphere even before it has started attracting matter or just a little matter at most. In case the question arises, why Itachi didn't use Amaterasu against Chibaku Tensei then, it was because he was backed up by Naruto and Bee and the narrative was Itachi teaching Naruto about relying on each other and teaching how every Jutsu has an exploitable weakness, hence them destroying Chibaku Tensei in a team effort. Itachi dealing with it on his own with disregard to Naruto and Bee would have been anti-climatic.
Against the repulsive force of Shinra Tensei, Susanoo would be more than sufficient for defensive purposes. Even the ribcage has proven to be incredibly durable, withstanding a punch from Tsunade with her seal released without being fully destroyed. Later stages would be even harder to crack, while the Yata mirror by virtue of its nature, would be able to block and reflect Shinra Tensei's force entirely.
Having the Totsuka blade on top, which is a spiritual weapon that cannot be absorbed by Gakido and that boasts incredible offensive power and the ability to seal away whatever it pierces, Itachi could very quickly decimate majority of the Pain bodies without them being able to do anything.
With us talking about a healthy version of Itachi, he wouldn't have problems spamming his techniques, given even a deadly sick Itachi off meds and at the latest stage of his sickness was able to use Tsukuyomi, endured it being broken, which visibly taxed him, used a large amount of continuous Amaterasu to set ablaze half of the Uchiha palace's roof, deleted Amaterasu, which also taxes the user and at the end utilized the last stage of Susanoo to decimate Orochimaru.
Itachi's powerful Mangekyo Sharingan aside, we also know that Itachi generally is an incredibly strong and talented fighter. Super fast, a great tactician and a master at using feints and deceiving the opponent, quickly to analyze the circumstances and act. Hence being an Anbu leader at the age of 13 and being said to reason like a Hokage at the age of 5.
As such, I'd give it to Itachi in both scenarios.