How universal are air traffic control systems, training and practices?
This question is analogous to asking, for example, how universal are law enforcement  systems, training and practices. At the highest levels you may find similarities driven by things like EU regulations, to pick one, but as you dive deeper into the implementation of those three things, you will find differences, from minor to wildly diverging. Police officers and air traffic controllers may receive very similar basic training, but once they move off from there and into the field, things can and will change dramatically. 

The same explanation holds for commercial pilots. A pilot flying cargo in Alaska on Cessna 185's, for example, will be trained in and execute procedures and practices completely different than a commercial pilot flying Britten-Norman Islanders on puddle jumping routes in the Caribbean.

Bottom line is it is challenging to answer this question without context, i.e. two countries you wish to compare.