What caused the major difficulties in uniting ancient Greeks under a single government?
At the height of their influence in the ancient world, Greek culture was organized around the "city-state." Certainly geographic influences would have shaped that development, each area being mostly a self-contained economic and political unit; the concept of a direct democracy kept the "politics" (literally, the affairs of the polis, or city) local. There was no need for any kind of overarching government; that would have been geographically and politically impossible, and would have been antithetical to democratic principles. Perhaps the reason Greece never became an Empire until the time of Alexander the Great boils down to the fact of its geography. These city-states upon which Greece was organized warred between themselves, the most salient conflict being between Athens and Sparta. Only when the whole of Hellenistic culture became threatened by Persia did they unite to fight, and that union eventually led to a brief Empire-like government until all of Greece became Roman.
First Ancient History, Oxford University Press, 2000, chapters 12 & 13.
I would say that the main obstacle to political unification in ancient Greece was geographical.
Greece is a very rugged country. There are chains of mountains that divide the land up into isolated valleys and plains. Greece also has lots of island, many of which are similarly mountainous.
This topography meant that the form of government that naturally sprang up was that of the polis, or city state. City states were walled off by nature from other city states. The topography made it hard for any one area to try to control any other.
So, topography and geography made it difficult to unify ancient Greece because it divided up the land and encouraged the development of fiercely independent city states.
The first and most likely major reason was the land of Greece itself. It was very mountainous and in being such literally separated Greeks from each other. Travel was difficult and so what occured was individual cities became city-states. In other words, cities ruled themselves without care or knowlegde of how other Greek city-states were running things. Laws and rules were different everywhere, and there truly was no way to unite ancient Greece as a single government. Another potential reason for Greece being unable to unite was that the city-states were rivals. Each individual city carried its own ways of life and pride, and change or reform into one government would have most likely been impossible even if traveling was easy.