Puerto Rico presented the problem of governance. There was a stark difference between the US fighting to "liberate" Cuba, and continuing to adminisiter Puerto Rico as a colony in the same way that Spain did.
The United States attempted to solve this by introducing limited self governance shortly after the war, and incrementally giving the Puerto Rican people more autonomy. The issue of Puerto Rican governance is still controversial today, with many people either calling for independence or statehood.