There would be a lot more ethnic diversity in 1899 America. I'm speculating, but I'm sure that the main reason statehood was not considered at the time was that they had populations with very few Anglo Saxons. Hawaii was still majority Hawaiian, whilst PR was - still is - majority Puerto Rican.
More speculating, but I would imagine that the majority of people in both places could not speak any English in 1899. It would take a big change in attitude for Congress then - or now - to admit 2 states where almost nobody spoke English.
Well, you are completely mistaken on a few points. The Hawaiian unfortunately were not the majority in Hawaii. There were large settlements of Japanese and Chinese that were brought in to work the sugar plantations (pineapple didn't come along until the early 20th century).
English was spoken in Hawaii to the point that most people were bilingual in Hawaiian and English. The same would be said about the Japanese and Chinese. They learned and spoke english while also funding their own language schools for their children. Just after annexation the territorial government closed and virtually banned the Hawaiian language.
The brakes that were placed upon statehood came directly from the white oligarchy that governed Hawaii since the overthrow. They wish to retain political power without extending the franchise to the Hawaiians and others. Basically it was a replay of what was happening (to a degree) in the American Deep South, but it was carried out by descendents of missionaries from New England. The territorial and early statehood days of Hawaii could give one an idea of what a country run by corporations would be like.
I don't really see Hawaii being much on the national scene until 1941.