One big effect visible today is the fact that Mexico is a contry with Spanish as the majority language. Additionally, the indigenous lost their culture and religion to a great extent and instead adopted the Spanish one.
The indigenous also mixed with Spanish and now Mexico is a land with many Mestizos, the mixed, and not as many indigenous.
I think Province or National
Phrenologists did not critically examine their data.
The settlements were an invasion of their land. The settlers took food, space, and resources that they had no natural right to.