I’m certainly no professional, but I recently took a class on Caribbean history with a big emphasis on Cuba and Puerto Rico so I can give a short and general answer. There was one big reason why Puerto Rico, Cuba, and the Philippines did not become states while places like Alaska and Hawaii did. It really comes down to late nineteenth and early twentieth centuries ideas of race. Cuba had a large black population and the United States’ aversion to this can be seen in their political activity and propaganda spread during the Spanish-American War. Basically, Hawaii had a large, white, English speaking population with a native population effectively under their control while Cuba, Puerto Rico, and the Philippines had large populations of Spanish speaking, non-white people who the United States did not want to become to citizens. I believe that Puerto Ricans were not recognized as US citizens until the 1920’s or 30’s. Cuba and the Philippines also put up much more resistance to American control.

There's always more to be said, but you may be interested in /u/The_Alaskan's answer to Why did Alaska and Hawaii become states but the Philippines, Puerto Rico, and the other Pacific islands did not?