This has two parts: I wish I were not too busy today to go in more detail but, as to the whole thing about us “voting down statehood to not pay taxes”, suffice to say there has never been a truly legally binding vote on it, those have always been part of a multiple-choice ballot, and the last few times the results were at best inconclusive; plus, on the tax side, once you do the net accounting of federal vs local credits, most of us would likely end up with about the same personal tax load – corporations of course are another tale, and they can pay more for ads and lobbyists.
In any case the argument about the vote that has been mentioned is mostly over whether the vote and representation at the federal level is an endowment of the individual citizens of the USA or of the citizenry as the polities of the states; that is more along the lines of the Electoral College vs. Popular Vote debate, when you think about it.
The second part is that yes, until Downes v. Bidwell, the Territories since the Northwest Ordinance had merely been divided into Unorganized and Organized, based on whether a formal local government and subdivisions had been put in place. The distinction of Incorporated vs. Unincorporated was a pure act of “Legislating from the Bench” in order to distinguish those 1898-99 acquisitions that were seen as not susceptible to being settled and assimilated with a view to make them become states some day, but just strategically sought as forward bases and extraction colonies. However, the records of the time DO indicate that this WAS influenced by how the peoples of the new possessions were seen as unsuited to become “real Americans” due to their ethnic and religious backgrounds and it DID create a “separate but equal” situation by which the “Incorporated Territories” would be considered irreversibly a part of the US homeland with a reasonable expectation of stewardship towards statehood, while the “unincorporated” would be sort of left hanging there as a mere possesion until further notice, or eventual divestiture (Phillippines).
Today the last Incorporated Territory is deserted Palmyra Island, which somehow was left outside the state of Hawaii. So on one of the issues, the point becomes whether the US should maintain the by now largely academic fiction of Incorporated vs. Unincorporated, with the stench of Plessy and of White Man’s Burden imperialism that underlay the doctrine, or the presumption that one word means your future defaults to eventual statehood. It can be argued that, for instance, all the federal legislation applied to Puerto Rico AFTER 1952 has had the effect of de-facto “incorporating” us in all but name, as for all everyday legal and practical purposes we function as a (flat broke) State except for the vote/representation and uniform taxes.
On the other point, that of the federal voting franchise being individual, that is a harder constitutional nut to crack. Unlike other federations the US contemplates one and only one class of Federal Constituency, the “several states” – there are no tiers of subcategory with different representation level. Mainland citizens temporarily abroad get to vote as absentees of the state which remains their US domicile of record, but if they move to one of the territories and officially change their residence there, they are as disenfranchised as us natives.
CGP Grey has an amusing video on the division of states, territories, and classes of territories here: American Empire - YouTube