What's the point with that quite lackluster story in Endwalker?

[Dikatis]

It'd be like if Aliens showed up on Earth, and one country's leader said, "Ah yeah, it's cool if y'all just settle anywhere you want, homies." Then the homies claim a continent or two, and start clearing out people that are in their way.

This is incorrect. The dragons of Meracydia were explicitly guardians of the continent who worked alongside mankind to repel Allagan conquest.

The native peoples of the southern continent banded together under the leadership of the dragons who also claimed dominion in Meracydia. While without equal on the Three Great Continents, the Imperial Army’s chimerical warbeasts were no match for the dragons’ fiery breath, and countless casualties were suffered. This, however, only served to further motivate the scientists of Allag in their ungodly pursuit of might through biological manipulation, and it was not long before they had created abominations which exceeded the might of the Meracydian Horde. In a decisive and bloody battle, the Allagans slew the dawn wyrm, Bahamut, paving the way for immediate occupation… or so they believed.

Together with my brood-brother Bahamut, I journeyed south to Meracydia. And together, we brought forth innumerable children into the world. We abided in peace, and all was well...until the men of Allag came, some five thousand years since. They slaughtered my children in droves, and took from me my beloved Bahamut.

The dragons didn't "clear out" anyone and lived in peace with the people of Meracydia just as the Ishgardians did with the Dravanian horde prior to Thordan's betrayal.

Please don't villainize the dragons for no reason.