Wish they had refrained from adding these decisions, or at least locked them to one of the fantasy focus paths.
Alaska and Hawaii didn't become states until 1959, well after the game's time frame. The reasons for them not being states were not changeable within the game's time frame. It's even worse with Puerto Rico, a territory which even today in 2018 is extremely unlikely to become a state any time soon.
I think the statehood issue should be framed within the proper historical context. Alaska and Hawaii were granted statehood - despite both having small populations and little resources (in contemporary estimates) - due to their strategic significance in the Pacific. As territories, one could make the argument that they would be relatively easy to snatch away from the USA through annexation, an independence movement, or as a result of the division of the USA in some Versailles-esque treaty. By making them states, you end any independence movement before it starts - as they now are not only officially a part of the United States proper, but also have full representation and all the autonomy the 10th Amendment can offer - and any attempt at annexation or balkanization becomes more difficult, in theory. The USA just flat out wanted to protect their ability to project power in the Pacific and Arctic, and statehood was just a means of securing that indefinitely. There is a big difference between whether Russian tanks are rolling across the Alaskan Territory or the State of Alaska, as only one of those can easily become the 'territory' of somebody else if the public grows tired of the conflict.
Puerto Rico, on the other hand, doesn't meet the same qualifications in our timeline. There was not, is not, and in the foreseeable future will not be any real challenger to US naval and air capabilities in the Caribbean, simply by virtue of all of the Gulf States existing. However, let's say those Gulf States became hostile; during the Second American Civil War that MtG seems to be themed around in part. Suddenly Puerto Rico gains much more significance for both the American Loyalists -as the island is now an unsinkable aircraft carrier sitting on the eastern edge of the Caribbean - and the Southern Rebels - if they want economic or military aid from any other part of the world. Germany wants to ship in troops? Aircraft, ships, and subs based out of Puerto Rico bar the way, probably even more so than Hawaii and Alaska do for the Japanese. Now, island combat in HOI4 is weak and just a matter of overwhelming the probably outnumbered garrison, and economic warfare is outright anemic for certain reasons; but the point still remains that if conditions are right, Puerto Rico becomes as strategically significant to the USA and its enemies as Hawaii or Guam. Would statehood be granted during the Second World War if nothing is going on in the Caribbean? Probably not, unless FDR feels like stacking something else in his favor. During a Civil War? We already have West Virginia and Nevada as precedent for that, and in both cases they were granted statehood purely to deny the territories to the CSA regardless of the outcome of the war. In a Second Civil War, Puerto Rico ending up a state is not at all unlikely - in fact it'd be quite prudent.
And looking at things from the other end, I doubt Puerto Rico would be too crazy about having a revived Southern confederacy - of any ideology - as its colonial master. So maybe the decision should be something like 'the Puerto Rican
Question', where whoever is in control of Puerto Rico after Civil War 2 plays out for lets say 3 to 6 months is able to either release PR as an independent puppet, grant statehood (with perhaps some pro's and con's, as I'm sure Hawaii would be first in line to demand they be given statehood as well), or 'delay the question' until the end of the war. Just flat out being able to grant Statehood without any reason to is... well, it's like granting Guam statehood out of the blue. Or granting Hawaii statehood in absence of Pearl Harbor. If WW2 never happened, statehood for any of these territories would likely never of happened. Status quo tends to be the status quo because it suits the people in power, but at the same time those same people will support change and reform if the benefits are readily apparent. That's the REAL reason why Puerto Rico is still a territory, even after numerous campaigns for both independence and statehood that the US Congress would probably support the outcome of, because the status quo will always be the safer option without some great necessity for change.