For any two given urban areas, their relationship is likely to be eitheras peers, that is, one competes with another (for labour, capital, and foreign trade), or as distinct members of a regional hierarchy (e.g., commuter suburb and commercial hub). And yes, depending on how you scope out regions, they may have different comparable roles. Note too that two suburbs within a given hierarchical region, say, Silver Spring, MD, and Arlington, VA, compete amongst one another within that region (Washington MSA).
In the case of Boston and NYC, you'd almost certainly see most transport and commute patterns within either city, with the inter-city transport being considered non-commute, for the most part.
More generally, this is why transportation networks almost always have to be designed, scoped, planned, and financed at least one level above the nodes they connect. Rome centrally managed highway construction throughout the Roman Empire, rather than leaving the decisions to local colonies and cities. In France and England, the first constructed transport systems, canals, were largely overseen as matters of national policy (though with private involvement), as was the Erie Canal in the United States. Development of railroads typically evolved similarly, with buildouts within specific nations in the US and Europe. This lead to a far more integrated system in the US (and USSR) given their much larger geographical area, whilst Europe's freight rail system remains much less capable than that of the United States.
* In the United States we know the answer, of course: rural areas have the power, and doing so would require them to cede that. One can dream, though.
Rural areas are poor, their industries have been gutted, and they are experiencing demographic death, as all the young people are forced to leave for urban areas in search of non-poverty level work.
It's not at all a tired argument, especially given:
1) the fact that the residents of smaller states get seriously-disproportionate presidential voting power in the Electoral College as a result of the two-senators-per-state rule --- in presidential elections, the votes of residents of any of seven small states (Delaware, South Dakota, Rhode Island, Alaska, North Dakota, Vermont, District of Columbia, and Wyoming) are weighted more than twice as much per person as the votes by residents of 13 larger states such as California, New York, Texas, Florida, etc.; [0] and
2) the fact that the Senate insists on keeping the 60-vote rules to open- or close debates, leading to frequent stonewalling of controversial matters.
[0] http://www.thegreenpapers.com/Census10/FedRep.phtml?sort=Ele...
Indeed; it was part of the Great Compromise. But that's not what you argued in your GP comment: By implication, you were claiming that this feature of the Constitution supposedly did not support the GGP comment's assertion that rural areas have significant political power (which to me seems well-nigh indisputable).