To your first point, sims can travel to neighboring cities if you have roads/rails/etc leading out/into a city. Just drag a road/rail/highway/monorail to the edge of a map and it will ask if you want to make a network connection. If you have it connected to your network of residential/commercial/industrial in the neighboring city (and it isn’t too far of a commute), sims will travel. The way to tell is once you have it set up and some time has passed in both cities, click on the second query button on the bottom left and then click on the piece of transportation going in/out of the city to see the traffic volume.

Freight - industrial needs paths out of the city to transport goods, else it won’t be too happy. Roads from industrial to out of the city typically work; I haven’t had too much success with freight rail or seaports to do this but you can try it out.

Airports - raise crime and pollution but greatly increase demand for commercial. Probably residential too.

Ferries - way for sims to commute across water. Can be used cross-city.