While an interesting skyline is nice, I think it's far from the best way to judge a city (I think there's also a pretty good thread somewhere comparing the various skylines of New England). I don't want to rank cities since my familiarity with most cities in New England is pretty limited, but I did want to comment on the latest Portland-Manchester debate. Let me first state my bias: I grew up in Manchester, it's where my family has lived for generations; I think both are great emerging cities, but Portland is considerably farther along in its renaissance.
First, as to the metro areas, I really don't think there's any way to accurately measure them objectively and say that Portland is larger. The Portland-South Portland-Biddeford MSA is considerably larger in land area than that of Manchester, and even combining Manchester-Nashua includes such distant, rural, non-commuter towns of New Ipswich while leaving out two of the largest towns in New Hampshire, Derry and Salem, which are both very tied to Manchester while being in the Lawrence MSA. Even Concord might reasonably be considered part of the same metro area as Manchester, and for planning purposes I'd argue should be. Portland's downtown is more cohesive, denser and more vibrant I'd say, but Portland becomes suburban much more quickly than Manchester. Portland off-the-peninsula is largely single-family, suburban development (granted mostly of the good, formerly streetcar, pre-war variety) whereas the neighborhoods surrounding downtown Manchester remain dense and walkable for several miles (or at least one mile depending on the direction). All that having been said, Portland is inarguably more important regionally; it is farther from Boston and therefore more self-sufficient.
Manchester's skyline is best viewed from the Amoskeag Bridge, or watching it unfold along 293 (which also allows a nice view of the lower, but at least as visually important Millyard). The taller buildings are not clustered as in many other cities, and are strung mostly in a line, but the view is still quite nice from the dense West Side, as well as from the hills of the East Side. I'd argue that the skyline is nice in some ways because it's spread out, with towers piercing the sky of an otherwise relatively low city more like the traditional church spires or even the clock towers of the Millyard. To that end, the view from downtown of the spire of Saint Marie's against the Uncanoonucs is quite nice. Manchester's skyline, especially when you take Saint Marie's and the millyard into account is nicer and more visible from around the city than Portland's, but Portland's downtown is considerably more vibrant. This gets to my point about the skyline as a measure of a city--Portland, despite lacking much of a skyline, is one of the most enjoyable cities to be in, whereas Hartford's dense skyline is arguably one of the least enjoyable downtowns to inhabit.
As I said, Portland seems to be considerably further along in becoming a vibrant urban center. This owes to a huge number of factors, not least of which is Portland's distance from Boston, its seaside location, and the fact that it is the cultural, tourism, economic and population center of the state. Manchester, on the other hand, has to compete with other Boston satellite cities, does not have as great a natural draw (though I'd argue that the Merrimack is an unharnessed draw), is not a tourist destination, and splits (at best) the cultural capital status with Portsmouth and maybe even Hanover.
Another big part of why Portland is further along I think is what Patrick said about their respective urban design. Manchester, by its nature as a planned city along a river and even more so by its later ill-guided redevelopment reads as largely linear whereas Portland is clustered and hemmed in on a peninsula. The urban renewal of the 1960s-1970s really decimated what would probably be some of the most vibrant, interesting and attractive areas of Manchester today: the Millyard, the Notre-Dame and Granite Square neighborhoods of the West Side, and vast portions of the edges of downtown. Not only would these areas probably be very attractive urban neighborhoods like those on the edges of Portland's downtown, but they would have greatly reduced the linearity of Manchester.
Hopefully future redevelopment and planning will help to remedy the errors of past planning initiatives. Combined with improved transit, regional planning, better zoning (recent changes to promote and strengthen neighborhoods, promote mixed-use, density and walkability are a good start), a further embrace of its recent ethnic diversity, and citizen initiatives, Manchester is poised to see huge improvements. While it currently lags behind Portland, more of the city is comprised of the sort of neighborhoods and buildings that once rehabbed (beginning to happen) will lead to wonderful, dense, lively neighborhoods.
In the end, though, I don't think it's possible to make an accurate comparison. Portland is far more of a regional center, but Manchester is considerably larger. If Manchester can better embrace its status as independent, regionally important satellite city of Boston, improve transit and planning regionally and within the city, and better incorporate Concord and Nashua as components of the metro-Manchester area as opposed to rivals, it is well positioned to be as vibrant, interesting and attractive a place to live and work as Portland. While I don't think they're that comparable, I do think the rivalry is healthy: both cities being able to contend for the capital of northern New England keeps them both on track for further improvement.
