To add to the links that /u/Searocksandtrees provided, let me say this: Only Alaska and Hawaii -- among territories with adequate population -- had a widespread popular movement for statehood.

In Alaska, this movement started almost as soon as the Klondike Gold Rush brought large numbers of people to the territory. The electoral platform of the 1914 Democratic candidates, for example, called for a drive toward statehood as one of its key planks. In later years, the statehood drive reached a practical fervor, with all of the state's major newspapers backing it, a large majority of the state's population supporting it, and strong political movements supporting it.

Despite this intense pressure from inside Alaska, forces Outside were able to block the statehood movement for almost a decade out of fear that Alaska Congressmen (as they eventually did) would vote against segregation. That's getting away from your core question, however.

The key difference between Alaska and Hawaii and Puerto Rico/the Philippines was the proportion of the population demanding statehood. Not until the 2012 referendum did a majority of Puerto Ricans favor statehood, and even those results have been contested, given the structure of the ballot question. For most of the period in which /r/askhistorians operates, a majority of Puerto Ricans have favored independence or continued commonwealth status.

In the Philippines, a strong majority has favored independence for as long as the polling record indicates. The same is true for other Manifest Destiny annexationist targets, such as Cuba and Nicaragua.

hi! more input is welcome; meanwhile check these out

• Why did only Hawaii become a state, while territories like Puerto Rico, Guam and Samoa acquired by the US during the same period remained only territories?

• Why caused American to only Annex Hawaii, but ignored its other island territories like Guam, Puerto Rico, American Samoa, Wake Island, or the Virgin Islands?

• Why didn't any of the non-contiguous American territories become states besides Alaska and Hawaii?

• Was the Philippines ever close to being considered a permanent territory for the United States, like Puerto Rico or Guam?

• Why was Hawai'i a state and not the Philippines ?

• Why were Hawaii and Alaska made states in the 1950's and not Puerto Rico?

• Why is Hawaii a U.S. State and not Puerto Rico?

• Why isn't Puerto Rico a U.S. state?

An interesting theory (albeit one I don't particularly buy) is put forward by Eric Love in Race Over Empire. Essentially he argues that US policymakers, whether they wanted statehood for these places or not, were hamstrung by larger culture which rejected incorporating so many foreign, "nonwhite" people into the US population.