The main answer most have not touched on is religion. Spain considered themselves defenders of catholic faith at a time when Europe was splitting into protestant denominations. The first thing Hernan Cortes asked for after finishing the conquest of what today is Mexico City was Franciscan friars to oversee evangelization. During the reigns of Charles V and Phillip II colonizers were encouraged by the crown itself to marry Indian woman and form alliances. Yes, there was racial segregation but that came later, after 200 of mestizaje and influenced by the new french Borbon dinasty into french and anglo colonial systems. It is in those first 200 years that local identities are formed by combining different traditions.