-After leaving the hospital, Estinien brought flowers to Azys Lla in memorial of Ysayle. He has since been traveling the world working as a mercenary in addition to helping the Alliance win the war for Ala Mhigo from afar. (He shows up again during the DRG 60 - 70 questline.)

-Shinryu and Omega both first appeared during the climax of 3.55. Shinryu was indeed the primal Papalymo bound.

-Nero disappeared from the narrative following the Crystal Tower and first reappeared during 3.4's closing scenes, seemingly having found Omega on the Cartenau Flats. (How he got there is a huge mystery.) Where he was and what he was doing in the interim is unknown; he describes himself as a "free agent."

-Hydaelyn is supposedly round like most planets; we see it from space during King Thordan's Ultimate End. As to why the Far East doesn't run on a different timezone... ¯\_(ツ)_/¯

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-Nero got out of the World of Darkness at the last second thanks to Cid literally lending him a hand.

-The Cartenau Flats are between Thanalan and Mor Dhona.