I agree that MSA gives a fairly accurate gauge for what's the most "important" city. However for measuring this particular exercise,I am on the fence about what measurement is best. I'd rather see "
urbanized area" (or a similar measurement) used. There's no question that judging the largest cities in each state based on their arbitrary civic boundaries is just plain stupid (like you, I often highlight Boston v. Jacksonville where Boston is a much larger urban area).
However, MSA numbers are based on boundaries that are essentially just as useless in New England-- Counties. All MSA numbers are is a total combined population of the counties that contain some residents who commute to the principal city(ies) in the metro area. It's fairly inaccurate in many cases nationwide (particularly in areas like the Mid-Atlantic where major metros overlap); but especially so in New England. What's more, is that if you include the entire MSA in many cases, a lot of somewhat autonomous cities are excluded.
For example, if you use MSA, you would exclude Cambridge, which is essentially a continuation of Boston's urbanized area and that's fine. However, you then exclude cities like Lowell, Haverhill, and Brockton. While those cities are certainly "satellite cities" of Boston now, they are still semi-autonomous urban areas. New Bedford, MA is technically part of Providence's MSA, but it crosses state lines and really isn't connected to Providence by unbroken strings of suburbs (Dartmouth, Westport, and Rehoboth are all fairly rural buffers between NB and PVD). I would say New Bedford is one of the more disconnected urban areas in a "metro" in New England.
The Portland MSA is a perfect example. Portland's MSA includes the entirety of York, Cumberland and Sagadahoc Counties. There's certainly no denying that Portland is the principal cultural and economic center for most of that area (Some of the border towns are more aligned with Rochester/Dover/Portsmouth) and the entire state, really (which is why its MSA numbers are fairly close to being accurate).However, Portland's MSA is perhaps the most rural in New England. It covers more than twice the land area of Rhode Island with only 514,000 people. Places like Sanford and even Biddeford are urban areas that are fairly disconnected (in terms of development and suburban sprawl) from the principal city. To take it further, I don't think places like Eliot, the Berwicks, Bridgeton, Shapleigh, Phippsburgh, Newfield, etc. resemble metropolitan or suburban towns by a long shot. Again, Portland is without question, the primary city for the majority of that area. However, when we discuss metropolitan areas, it's usually in the context of a city (or cities) and its suburbs. Using the Portland MSA would exclude Biddeford and Sanford which are small, but notable urban areas in Maine.
Using Urbanized Area which incorporates the principal city with its unbroken string of suburbs would allow us to exclude suburban towns (i.e. Scarborough ME, Warwick RI, etc) and count the semi independent smaller cities that are slightly disconnected from the core of the metro (i.e. New Bedford, Sanford, etc) as well as those much smaller cities that are overshadowed by more spread out suburbs (i.e. Portsmouth NH and Newport RI). Unfortunately, as no system is perfect, places like Biddeford, Lowell, Lawrence, etc... are all included as part of a larger "urbanized area."
That's pretty impressive. Vermont was just so tough to calculate. To be fair, I think Rhode Island's (not Maine or NH) was the most infested with auto-oriented suburban municipalities. Pawtucket is an urban extension of Providence (much like Cambridge is to Boston), but much of what else is counted around PVD is auto-centric suburbia (most of Warwick, West Warwick, much of Cranston, most of North Providence, a lot of East Providence, and Coventry). With most of Maine and NH, those towns have town centers and some unique characteristics. Many of the RI towns don't. I HATE West Warwick with a passion (had family there while growing up). Pawtucket is kind of cool, but Cranston, Warwick, N. Prov. and East Prov. are "meh." Coventry is fairly rural in character.