Wow - thank you for such a detailed response!!
I shall break down your response, with any follow-up questions I have...
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Overall, remember that SimCity is utilizing an agent pathing program that is rather flawed in the simulation. A particular Sim does not choose a particular job or building to go to every day; workers will exit their building and follow the path of least resistance until they find an open job.
I was very disappointed to learn this some time ago. I was browsing through SimCity tutorials and found one explaining how the agent path works...a shame to say the least.
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This can lead to weird things like Sims waiting at a bus stop that's set right outside their door, jumping on the bus and exiting at the next stop. If there's no employment at the next stop, they'll just wait at that stop for the bus to pick them up and carry them to the next one. If this is at the end of a road, for instance, they can spend all day going back and forth between two bus stops, never finding the industrial area that is on the other side of the city.
This is good to know. I have 10K of my population regularly riding buses, so if they're travelling from one stop to another within the same road perhaps that is why Commercial buildings are being abandoned, with no workers or shoppers actually attending them!
wrote: In every case, try to build so that Sims have to walk rather than drive or use mass transportation. Aim for an RCI ratio of about 3:1:1. Build residential zones with the commercial mixed in; R on the ends with a section of C in the middle works very well.
Please could you explain this ratio to me further? Do you mean 3 residential buildings to 1 commercial? Is that low, medium or high density or reflected throughout?
I find that SimCity lacks certain detailed information. I have the Extended Data Mod so I know how many workers are required for Commercial and Industrial buildings, but what would be good to know is how much freight is provided per building and how many goods are sold.
I have deduced that a low density Industrial building is either 60, or 80 freight. Medium is 120 and High is 240 - although a high density industrial building is the same size as two medium so provides little value!
I also know that a low density commercial building provides shopping for 7. But I don't know about Medium or High density.
I don't know whether med-tech or high-tech industry provides more freight, or just cleaner production of it...
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Build dorms for your university and lay paths to the main building so the students walk to school. As far as these paths go, you can use them all over the city and all sims will use them. They're free to lay and give your Sims walking options, so use them! (Also helpful - garbage trucks will use service roads and avoid mucking up traffic if you lay them around the city as well)
How far will Sims walk? Can you provide me an estimated distance and how to gauge it within the game?
Do the trucks use the service roads in favour of the other types? That is helpful to know because seeing cars queued behind a truck collecting garbage is a painful sight 
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If you have a university, do not place any other school building types or school bus stops. There is no distinction between elementary school students and university students. All of the student agents are just "students". It's cheaper and better management in the long run to build multiple schools (whatever type you're using) placed around the city so that students will walk to school. University students will will either walk (good) or drive (horrible traffic) to school. They do not use public transportation. Use the dorms to fill your classes so you don't have regional "students" flooding in and mucking up your roads.
I do have a University - so that my Electronics buildings are more efficient - and I placed the building far from my main City spread with a singular road to and from. I was amazed, and a little concerned, with how much traffic that actually generates! Hundreds and hundreds of cars all queuing on that one road, waiting to spread amongst my Residential area.
I've now shut down most of the University, to minimise how many students can attend. The City is less educated, but there is less traffic on the road now, at least.
wrote: Bus terminals, trains, planes and boats - all are "regional" traffic. They'll bring in tourists and possibly carry off some of your unemployed sims, who will never find their way back. If you are running anything besides a tourist or gambling city, I would recommend that you demolish the bus terminals (turn them off and wait at least a full sim-day to make sure the buses get back to the garage before you bulldoze it). If you need the tourists for an area, set the bus terminal or ferry by the casino or landmark and don't use any bus stops or buses. This will force your tourists to walk right to the landmark and leave by the transportation method. If you don't do this, when they leave they will generate hundreds of taxis to take them out of the city. Think of regional transport as bringing sims in - they do not help with city traffic flow or resident transport.
Thank you for this incredibly helpful piece of knowledge. I always thought of SimCity as replacing old and cheap with new and expensive. So always replace Shuttle Bus Depots with Municipal Bus Terminals. Plus, the descriptions themselves suggest that it'll help with commuting and traffic.
If I built a train station in the Residential area and a second in the Industrial, what will happen to the commuters then? Or do they just carry on and out of the City?
Similarly to a previous question - how far will tourists walk? I read or watched somewhere that having a Municipal Bus Terminal (MBT) placed at one side of the casinos and a second MBT placed at the other side will make the tourists get off from one and walk passed all the casinos (visiting them to spend money as required) and get on at the other to leave?
Also, if the MBT brings in Sims from the Region and you've advised not placing bus stops for residents...how many bus shelters at the MBT should be placed? None?
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In cases where you need transport for your city Sims, use shuttle buses, streetcars and park-n-rides. I usually have my Industrial set on the downwind side of the city, and the Residential and Commercial together on the other side. It works great to have shuttle bus stops and park-n-rides right in the center of each area, maybe a streetcar avenue down the center of the city. Only put stops right where you want the sims to go. So a line of Industrial buildings with a shuttle bus stop in the center, and park-n-rides on either side, that sort of thing. It seems counter intuitive, but the less stops scattered about, the better. Place them with intent and purpose, and they will work well.
I am slightly unsure about how and where to place bus stops...so I shall explain how I have placed mine and receive your feedback about whether this is correct. So, on one stretch of road where I have 8 high density Residential buildings I have placed 4 bus stops. One stop between two of the residential buildings.
On another stretch of road, away from this, I have 10 high density Commercial buildings and have placed one bus stop between two of these, totalling 5 stops.
On another stretch of road, away from both, I have placed 1 bus stop outside a high density Industrial building.
Which of these will work, and which won't? Which of these will cause passengers to jump between stops, one after another.
wrote: Try to create "straight shots" for anything that has to either enter the city or exit the city. This means trade depots set very close to the city entrance in order to get your goods exported or imported as quickly as possible; try having an L-shaped road at your entrance with a straight shot to trade depot.
Finally something that I am well knowledgeable of. I learnt this from my first City build. Nothing more frustrating that seeing that goods required are sat in three hours of tailback traffic. What I have found is that using the UDoN mod, is that a delivery van will drive out of its garage and around the block before returning to the depot to pick up the goods. I think this is based on the design of the depot itself, where it isn't self-contained and actually requires the delivery van to move out on to the road before collecting goods.
wrote: There are a couple of bugs that happen fairly reliably; student agents go missing (especially with universities) and the only way to get them back is to demolish the building and let it rebuild. Worker and shopper agents may also disappear, usually exiting to the region for something, never to return. Again, demolishing the building is sometimes your only resort.
How can you work out if Student agents or Worker / Shopper agents have gone missing?
I do appreciate all of the help you are offering and apologise that each answer produces more questions!