Puerto Rico, which became an American protectorate under the Treaty of Paris, was very poor. US troops were welcomed in 1898, and the Puerto Ricans greatest hopes were for increased rights and a better economy. Puerto Rico's experience under US rule was more positive than that of the Philippines. In 1900, Congress passed the Foraker Act, which set up a civil government for the Puerto Ricans, and gave the Puerto Ricans some amount of self-government. However, most power still belonged to officials appointed by the US government, a fact which angered many Puerto Rican natives. The US went right on working to Americanize Puerto Rico, importing institutions, language, political systems, and the like. However, the US was always vague about Puerto Rico's eventual political future. As a result, a resistance movement sprung up, led by Luis Munoz Rivera. Gradually, the US granted more and more concessions to the Puerto Ricans, and in 1917, Puerto Ricans were made US citizens, with full citizens' rights. In addition, the Puerto Rican immigrant community in the US was largely a result of the relationship that developed between the US and Puerto Rico as a result of the Spanish-American War.
In Cuba, the US installed a temporary military government after the war. At first, General John Brooks was sent in as leader of the occupation government, but he proved too antagonistic to the Cuban population. The US soon installed a second occupation government under the direction of the former leader of the Rough Riders, the newly promoted General Leonard Wood. Wood's main goal was to improve Cuban life. He modernized education, agriculture, government, healthcare, and so forth. Wood also had Havana's harbor deepened, in preparation for a higher volume of trade with the US. At the same time, research by Dr. Walter Reed, begun during the war, located the mosquito that carried yellow fever. Wood followed Reed's advice, and destroyed many of the swamps, marshes, and pools of water where these mosquitoes bred, reducing the frequency of yellow fever cases.
But although Wood seemed to have a knack for Cuban government, and the US would probably have liked to keep the island, there still was the problem of the Teller Amendment. In 1902, the US did indeed honor its promise in the Teller Amendment, and, while it did not withdraw from the Philippines or Puerto Rico or Guam, did withdraw from Cuba. However, afraid that another great power might conquer Cuba, the US forced the Cubans to write the Platt Amendment into their new constitution, which was ratified in 1901. Among other things, the Platt Amendment gave the US a Cuban base (Guantanamo) that remains to this day. The Cubans, although they always followed the Platt Amendment, deeply resented that the US left a military base behind, which they did not feel truly lived up to the Teller Amendment's promise to withdraw entirely from Cuba after the war.
For Puerto Rico, life as a US protectorate had its ups and downs. On the positive side, the US improved many areas of Puerto Rican life, providing more education, improving sanitation, and building roads. On the negative side, there always were a certain number of Puerto Ricans who chafed under American rule and who desired independence from the US, such as Luis Munoz Rivera and his resistance movement. Nonetheless, Puerto-Rican American relations were far more peaceful than US-Philippine relations.
A problematic legal issue arose over the fate of the Philippines and Puerto Rico. As protectorates, many wondered, did the US Constitution apply to the people there or not? The dispute was finally cleared up in a series of 1901 decisions known as the Insular Cases, in which the Supreme Court found that the Constitution and other US laws did not necessarily apply to colonies. Because of the decision, the task of deciding which US laws did and did not apply to the colonies fell to Congress.
General Leonard Wood's Cuban occupation seemed fairly reasonable and willing to compromise, except for one major blemish. When Wood set up the occupation government, which granted some small amount of self-government to the Cubans, he put structures in place so that Afro-Cubans would be kept out of politics.