Thalassicus
Bytes and Nibblers
The problem is that you have no alternative to put your hammers into once you build all the buildings you desire. Hammers are only converted 10% into gold or 25% into science. So you might as well build culture buildings to do something useful with your hammers.
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Not all cities should have all buildings. For example I build a city in the middle of the desert to get an oil resource. That city would never grow without a granary. Also in my production cities for units and wonders, I do not want my population in farms but rather in mines. So I build the granary and watermill there to have more free pop at the hammers. The culture is not useless. SP can make a huge difference in science, military and production (Communism for example gives you 5 hammers in every city!). You have to get there somehow and if you have a large empire, it is quite useful to have some cities devoted to culture in order to get the SP you desire. Of course, if you play Civ5 like Civ4 and build everything everywhere, you digg your self a nice and deep grave.
I agree with both your points. If maritime city state bonuses are reduced, granaries might be useful. Free food to every city the moment it's founded somewhat outshadows it right now.
Here's my main thought.
A game is a series of interesting choices, and the choices do not feel interesting. In IV buildings were useful in almost every city, so you had to make valuable build-order choices. Focus on culture for borders, research for cottages, production for later building, or defense from potential conquest? The fundamentals of 4x.
Right now the later science, culture and defense options just don't appear valuable choices for the majority of cities, limiting options to money and happiness spam.