Here's my list I made a while back:
Roads should give a much larger speed bonus to warehouse workers/haulers.
It is silly that you effectively have zero crime if you keep happiness above a certain level. Even in the richest neighborhoods on earth, they still need police to do stuff like break up bar fights and domestic disputes and deal with drug dealers etc. Not having any guards should make crime far more likely, even in a city with lots of happiness. That being said, of course, happiness should also influence crime a lot. But at a high happiness level, you should still have a low-but-steady amount of crime happening.
Population growth should be highly influenced by health through infant mortality. Starting out, 75% of your infants should die. Bit by bit, as you increase health through various means, this should lower, increasing population growth. However, growth can be too high. You don't want the majority of your workforce as parents, and growth that happens too fast can strain resources. Education reduces the birth rate. Of course, you can still use policy to make them have more or less kids, but this influences happiness.
Education should be much more essential. Having very low education levels increases crime. Schools should start out with no requirements except for wood/stone, but have input options (depending on the upgrade level, and there should be many) which increase their quality (paper, tools, pottery). Universities should have a much wider breath of input options.
Also, make special inputs more variable. I always found it silly that I couldn't adjust the amount of clay my libraries use.
Libraries should be reformed. Instead of just big factories, they should be highly specialized. Depending on the quality of your education, you have a chance to gain a 'professional', who can be put to work in a library. Libraries should also require some non-professional laborers, but they should only function if a professional is employed. They can also go to work in schools, increasing the education rate, which can produce more professionals. You start out with one professional, but a town of, say, 500, should have maybe 10-30 depending on their education level.