This sort of feeds in to the whole 'Snowballing' argument or the 'Bigger doesn't necessarily equal Better' argument.
For instance, consider the following:
(A) Nation which covers a large landmass (Lots of Cities): Such a nation will
(a) need a large military to defend its borders and keep order in its outlying 'provinces' (higher costs).
(b) need more 'connective' infrastructure (higher costs).
(c) Will suffer from higher internal instability-especially at the fringes.
(d) More chance of culture from your core cities 'diffusing' before they can reach your outlying areas-this can also contribute to the instability mentioned in (c).
(e) More demand for Finite Strategic Resources.
(f) Transport of goods (food/money and shields) is less efficient.
(B) Nation which has a high population: Such a nation will
(a) Suffer more from overpopulation, pollution, crime and corruption-and possibly also poverty.
(b) Greater demand for Finite Luxury Resources.
(c) Need more food to support your people to avoid starvation-this can mean harsh rationing (happiness cost), or seeking food through trade (monetary cost).
(d) Greater demand for 'material wealth' in the form of shield and food-which must therefore be directed away from other activities such as sustaining population growth and building improvements/units.
(e) High Population cities would need more frequent upgrades of internal 'infrastructure' in order to avoid many of the difficulties described in (a)-(higher costs).
(C) A nation with a very high level of wealth/research: Such a nation will
(a) Wealthy and/or technologically advanced nations will tend to have more 'demanding populations', i.e. they will tend to need more 'consumer goods' to remain content.
(b) Some sections of society will want the fruits of technological success to be applied more 'ruthlessly', wheras other sectors of society might be afraid of rapid advancement, and seek to prevent you applying recent advances.
(c) wealthier societies tend to suffer more from corruption and, to a lesser extent, crime-especially if some cities have wealth that is well below the 'national average'.
(d) high tech improvements and units often have a lesser manpower requirement, thus leading to a potential increase in unemployment-which kind of feeds into (b) to some extent!
(e) nations neighbouring more advanced and/or wealthy nations may become jealous, and demand a slice of the pie (even to the exent of ganging up with other, less powerful, nations!)
The key issue here, though, is that good players CAN manage the vast bulk of these issues-to the extent that their nations can survive, and even THRIVE, in spite of their large size, population or technological/commercial success. Yet having to manage these difficulties helps to curb 'runaway success' whilst allowing more compact and easily managed nations to stay 'on par' with their larger rivals.
Anyway, hope that all makes sense

!
Yours,
Aussie_Lurker.