Once again writing a bit beyond my specialty here, but I think I can shed some insight. I'm drawing from Michael Wilrich, Pox: An American History, so my answer will be narrow in a number of ways.
Puerto Rico and the Philippines had two very different colonial experiences, so this is not as apples-to-apples as you might think. First, we can look at how they two places entered the American orbit during the Spanish-American War. Puerto Rico was one of the US's easier acquisitions during the war, and saw no major fighting as the US replaced Spain as the island's colonial master. Most Puerto Ricans were willing to work with and recognize the American government, and often viewed it as something of a improvement over Spain.
In the Phillipines, an American fleet arrived just as Filipino rebels were about to overthrow the Spanish government. The commander of Spanish forces in Manilla made a catastrophic decision to try to break past the American fleet, resulting in a total defeat for the Spanish. He then surrendered the colony to the Americans, who were more than happy to accept. By way of comparison, it would be like if the the British surrendered to the French at Yorktown, causing he US to become a French colony. Filipinos were understandably furious, but they had little by way of legal recourse.
As a result, many Filipinos continued to fight the urge to colonial power - in this case , the US. The Americas responded by sending thousands of soldiers to occupy the island, and they stayed there until WW2. This was a cruel, bloody guerrilla war, and American excesses were as frequent as they were horrific. The Philippine colonial experience was one of *constant, intrusive American presence and domination. Even though many Filipinos hated American control, many could not go about their daily lives without a encountering and operating within the context of American culture, particularly military culture.
Puerto Rico, on the other hand, cooperated with American control. As such, the United States did little to meddle in the internal affairs of the island beyond installing a governor. The Puerto Rican experience was one of cooperation and collaboration as the US worked with local officials to build roads, public schools, and a health system. America's imperial presence was thus a light touch that did not enter the daily lives of most Puerto Ricans, and the US made no serious effort to try to change or eradicate Puerto Rican culture.
I have to ask: In which way did the Philipines embrace English that Puerto Rico didn't?