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.
The road advisor deeply cares that all of your buildings be attached to the region. If any buildings are not connected, he will complain that there is no region access. In the above picture, I have demolished some roads and some decorative cinderblocks are left behind. Since this former decorative part of an industrial zone has no road, it has no region access.
If you hover over the little triangle by the advisor's head, then click on the little red road icon, you can cycle through the occurrences of such buildings. This works for fires, crimes and abandoned buildings as well, from their advisors.
I have tried to connect my cinderblocks to a road, but the roads do not cooperate. As a decorative building, it's immune to direct bulldozing. I just let the road advisor worry about it.
Best Answer
The municipal airport provides limited functionality when connecting cities. It does not allow the exchange of utilities such as power, water, and sewage because those agents move via road. It also does not allow you to share city services, as those need to travel along roads. It will however, allow workers, shoppers, and tourists to move between cities. It will also ship Freight between cities.
It will raise the happiness of any industrial buildings in proximity, but make any residents nearby unhappy presumably due to noise.
It can be expanded to generate more tourists and higher wealth tourists as well, in fact, adding a municipal airport (or the international airport great work)seems to be the single best way to increase high income tourist traffic.