Pretty much all the central American civilizations were a rough collection of City states (particularly the Mayans and pre Aztec civilizations).
Rio certainly meet similar criteria as Sydney and co. If you really feel that more than half are parts of true civilizations, I'd be happy to discuss them if you're willing to offer explanation for each.
Well, the definition of city-states I'm familiar with derives mainly from the italian republics: Autonomous communities with it's own set of rules and definition of citizenship.
Rio just doen't fit. I just cannot see the correlation. It was a colonial center, then imperial capital. It doen't fit a single criteria.
La Venta, deriving from a completely different cultural panorama couldn't be even remotely compared to that definition (and that leaving aside the fact that the city was part of a much major complex and, by no means, as independent as a possible 'expanded' idea of city-state might accept).
And Lisbon, altought more independent than the other two for quite a while, was never autonomous, as far as i know.
I don't actually feel more than half are part of actual civilizations. I just do not see, in them, the degree of characterization to be considered, by itself, an independent political community. They are part of a complex, even if that complex does not constitute a civilization.
(It's not that the game's take on city-states is wrong or anything. It's a game, it needs to make things simple... It's just that i really feel any city with some historical background could fit the developers criteria for city-states. They needn't be actual city-states)