What you are seeing is working as intended. Not all cities within a region will be able to share all things but they are eventually able to share most things. The most limited of what can and can not be shared are going to be water, sewage, power and garbage. These are limited by physical roads. This is where you get your cluster or sub-region as you have noted. The best way to tell which cities will be able to share these resources is to see which ones are connected by road as roads are needed to transport these materials.
In the early game this can also hinder almost all resource transfer. You can eventually unlock things like a trade port that can use roads or rail or water to transfer resources locally or globally. There are also additional methods for the transportation of people and such via ferries and the like. The last thing, that jumps the final gap, is an air port.
These things together will let other cities be more connected but it should be noted that anything that requires a road, as mentioned above, will never be able to get to another city that does not have a road connecting to it.
EDIT: Found out last night that gifting also requires a connection between the cities. Even the act of sending money from city to city required at least a rail connection between the regions. I have not seen if ferries or air ports will fulfill this requirement and will update here when I figure that out!
Great Works are region wide as well. If you unlock a great work like the solar farm in one sub-region you are then capable of building that great work at any site on the map. However note that getting resources to a remote location may be a bit of a challenge.
This also works with other unlocks that claim 'region wide' like the upgrades to City Hall. Even though the cities are not connected in any manner people starting up cities in other sub-regions or clusters have access to 100,000 bonds for instance.. Smelting plants and the like. So it does appear that development unlocks also jump over the bounds of a solid (or even liquid) connection.