How is it that the Dunmer have Almalexia, Dagoth Ur, Sotha Sil, and Vivec who have god-like powers yet they get over-run by lizards?
The lizards apparently have their own god-like entities in the Hist, who are powerful enough to compel people to just stand still and let themselves be killed when Umbriel attacked instead of fight back or flee. And that was just one of them acting alone.
The An-Xileel and their renegade tree seem to have taken over Dagoth Ur's "death to the N'wah" plan and had better success with it. I imagine this wouldn't win them many friends among the Argonians outside of Black Marsh, who would've also been killed for being too Imperialized. So some Argonians in Skyrim might've been fleeing Black Marsh and be more sympathetic to the Dunmer side. It wouldn't surprise me if the Argonians could be facing their own civil war as well.