When you compare the Philippines to Hispanic America it seems the Philipppines retained so much of their indigenous culture. Filipinos all speak their indigenous pre-colonial languages and most of them are not mestizos or white due to mass rape. I read somewhere that something like 1% of Filipinos can even speak the Spanish language, which is obviously a huge contrast to countries like Mexico and Peru.
I get the impression there was just total genocide of the Aztec or Mayan cultures and people when the Spanish arrived in the Americas. Most of the indigenous people died and they lost most of their culture.
Why were the two regions treated so differently? Or why do they look so different today (culturally and linguistically)? Today you could go to the Philippines and not even realise it was a Spanish colony for centuries.
You have a mistaken impression about the Spanish conquest. I don't know much about the Mayans and others, but the Spanish didn't genocide the Aztecs, though in other cases, like with the Pueblo, there's certainly a case to be made for genocide.
The reasons so many Aztecs died were primarily diseases. It's not really clear how many died, but one estimate made by historians at Berkeley University even puts it at 95% of the Aztec population dying because of repeated epidemics. Admittedly, the early Spanish colonial system was filled with abuse as the conquistadors formed their own fiefdoms with the Indians as their servants, a system called the encomienda system, but that system was abolished relatively quickly and replaced by a much more benign system, where Indians generally were left to rule themselves in their own communities, called pueblos de indios, or at least be ruled by Indian mayors called gobernador de indios, who were in turn elected by the local Indian nobility, the caciques, alongside a Spanish administrator called a corregidor.
Mestizos aren't the product of mass rape, they're the product of simply intermixing over the course of several centuries. It's the same reason you have Afro-Indians and Afro-Europeans in Mexico. The early Spanish conquistadors didn't bring their wives along, so they just started marrying native women. Same with slaves and Indians and slaves and Europeans. Though the Spaniards had instituted a racial caste system, race was such a vague system that it was practically useless. Indian nobles were above a poor Spanish farmer de facto, and a village full of black people could be classified as an Indian village simply on basis of location.
In general, the Spanish king had a very paternalistic view towards Indians, so if they were abused he did try to help them generally, although it was from a somewhat misguided point of view. There are still hundreds of letters in Spain between Indians nobles appealing their cases to the Spanish king. This was one of the reasons the Spanish king abolished the encomienda system, alongside the more practical reason that he didn't want the conquistadors to form independant kingdoms in the New World.