Hmm, I actually think plopping several size 1 or 2 cities around is very adventaeous for the scions already, so I don't think the 'Edit 2' suggesiton of granting an additional awakening bonus is a good idea. If you plop a city on a hills plains for the extra 1 production in the city square(better if its a marble hills plains for three production), which has a good spot in its fat cross (say, copper in a hills, patrian artifacts, gold, something like that) you've instantly got a city with decent enough production to eventually crank out the awakening spawning buildings (which all told will cause that city to contribute an additional base 3.5% to your awakening chance) while raking in substantial comerce (if gold, artifiacts, etc). Also, once you've got trade, currency, etc (especially if coastal) its going to be pulling in alot of trade....well outweighs the maintenence and the value of an additional pop in your capital. I usually don't get around to creating a super capital until I've expanded to my defensible limits...
I agree the crowding mechanic is not urgent - seems like a very difficult balancing problem that will lead to a complex forumla that might have unintended effects...Besides, tons of game options already power up or down civs anyway, without too much of a cry for balancing. In the scions case, heres a few examples. Blessings of Amathon helps other civs more than the scions, as for awhile you'll lack the pop to work most of your recources anyway and many of the recources are tied to health and give food plusses. Raging Barbarians helps the scions significantly (period incursions of 5 stacked goblins or orcs is a christmas present for your legates). End of Winter helps the scions significantly (hampering the early phase for everyone, scions are less hampered because of food, and stretches out an early period of spawning). Other civs it is easy to dream up examples too (I'll go for the lazy example of the lanun and the amount of water...). I think a nice understandable formula based on map size, and then you know where things are going when you choose game options, map size, difficulty, etc...
Edit - on the size 1 cities comment, to explain in more detail what I am talking about - tailor your research to get code of laws early, switch to aristocracy, and then pick up drama pretty early (though after bronze working so koriana can protect you), while having every city but your capital build shrine to kyorlin, temple of the gift, then hall of the covenent, and let your capital handle building anything else. Its an effective way to play the scions in a builder, expansive, awakening focusesed manner. Not that it works any better or worse than a god king military expansive manner, but its a legitmate strategy and probably not in need to an awakening bonus from territory controled.