#3. You are not specializing your cities. Jack-of-all-trade cities are highly inefficient.
a. Early in the game, you only need one super science city in an optimal site to do all of your research and keep up. (Food + Library + academy + scientist specialists) Scientific progress is by beaker count, not by that percentage number. What is better? 100% of 10 raw beakers or 50% of 30 raw beakers?
b. Set up one or two high production cities (food + forge + hills + forests) to provide your unit needs, and the rest can be money (food + market + merchants) or science sites. Large numbers of mediocre cities will kill your science rate. Build only units in high production cities, science in your science cities, and money in your money cities... Units can move. Building a unit where you are getting massive science multipliers is a waste of resources.
That's all I got.
Ok... but all cities must have enough food to work tiles. So, production cities that use mine's, must have the food resources to have those mines worked; commerce cities must have food to have the cottages worked.
But what about the science city? What factors are used in the science city????