The most important long term impact of Spanish systems of integration was that they created very hierarchical societies that had very little in the way of democratic tendencies.
The Spanish systems of integration were designed to put the Spaniards on top of the social pyramid. The encomienda system, for example, gave Spaniards complete control of the lives and the economic output of the natives on the lands given to the individual Spaniards. The Spanish created a society where it was expected that there would be lords ruling over vast numbers of peasants. This helped lead to the creation of societies (such as that of independent Mexico) where local and national strong men were able to dominate politics, economics and society and where there was little taste for democracy or egalitarian ideas.
The Spanish system, then, helped to create a society that was very hierarchical (at least partly on racial lines) and undemocratic.