Lately I started experimenting with a strict hub&spoke design. That means that all lines have only two stations, Start and End, where Start is the point the vessel is waiting until completely loaded. I wanted to design a map where the vessels are running only if 100% loaded.
Some results so far:
Passenger transport works best if you are putting the Start station to the sub-urb or the small town and the End to the big city or large station. It seems that objects constantly generate more passengers (and mail) than they receive. Thus you have to wait at spoke end and then travel to the hub (and there you pick up all waiting passengers back to the spoke without additional wait time). But sometimes you still get congestions at single stations and thus have very unbalanced lines, thus I found that setting the "wait till" to 50% works much smoother because this can deal even with objects which receive up to twice the amount of passengers and mails than they generate. If some lines are so crowded that you can run a second vessel it often make sense to put it into a line with reversed Start and End station. Interestingly though it makes sense to go for maximum capacity of vessels rather than speed.
Industry networks are easy at the beginning, because all goods have defined sources and sinks. Thus you design your lines to wait at the source and go to the sink. But some industries have products of the same class than the goods they are taking. Saw mills for instance take wood and create wood. Same with printing presses, which take goods (printing colors) and create goods (books) of the class "bulk".
As soon as production networks start to overlay each other, you run into logistic problems, as you can have pairs of stations which both take and offer the same type of good, requiring you to have two lines for the same type of good with reverse Start and End.
This forces you to build extremely large stations to have enough loading bays for the waiting trains. If you need more than one vessel per line to cope with the amount of goods you have to deliver, you also need parking room for the currently empty vessels which are waiting for their loading bay to become empty, as you cannot easily warrant for a steady flow of goods.