I quote from a somewhat dated source, the "DK Essential World Atlas" (1999), which states:
America's overseas territories have been seen as strategically useful, if expensive, links with its "backyards." The US has, in most cases, given the local population a say in deciding their own status. A US Commonwealth territory, such as Puerto Rico, has a greater level of independence than that of a US unincorporated or external territory.
I highlight the part that most caught my attention. Looking at the list of territories, what stands out is that neither population size nor location appears to be decisive in determining status. For instance, Guam (claimed 1898, population (in 1999) 144,000) is an unincorporated territory, whereas Northern Mariana Islands (claimed 1947, similar total area to Guam, pop 47,000) is a Commonwealth. Virgin Islands (claimed 1917), comparable area and twice the population (1999) of the Marianas is like Guam unincorporated. Puerto Rico, with its large population and proximity to mainland USA, seems an outlier. It is sensibly a Commonwealth and could presumably become a state someday if some get their way.
Can one generalize and say that there is a general coherent set of guidelines that determine what territories have been assigned particular status by the USA? Naturally historical events are at play, but is there more than "accident" involved?