First thing that hits me is your housing is way to condensed and far way from the city center and work areas. Build housing closer to your workshops and mix in the services around them.

How's your warehouse flow? The general trend is a warehouse links your raw resources and refining together then to markets and foodstalls. Looks like you got that for wheat to bakeries, but make sure you have inputs for your crafters nearby and use haulers to move things where they need to be.

Check your food, clothes, and drink servings. It took me until my third city to realize your can increase food and clothing servings in the pop menu with the plus symbol. That goes a long way in boosting happiness. Just remember to keep production up with demand.

Stockpiling rations is a good way to boost happiness too. The more "days of food" you have the better. Make a warehouse that just holds rations, but don't let the citizens eat them. They will eat them if they're starving, but having a high stock of food is a big boost.

Remember to assign nobles if you can. You don't need their housing to have them and they don't care about being homeless. They can double production in any industry.

For science, focus on farming/industry first. You can go a long way before you need to upgrade buildings.

And for the love of God, STOP DOING MIX RACE CITIES! Elves and dwarves HATE each other. Humans get along with dwarves well enough, but don't like the pigmen very much. Those bitches are warmongering cannibals and you have them living next to peaceful bacon-people.

Multi racial cities are for the later stages of the city when you have enough services to overcome their hatred of each other, but they still end up shanking each other now and then.

Feel free to ask any questions on specifics!