Well, firstly it made all-year conflicts possible instead of seasonal campaigns, when the professional soldiers didn't have to return field-working. Secondly, with a standing army it was possible to cover the broad borders of the nation as it grew from a city state.
With a milita-army reaction times were also slower, as generals had to first muster up and train his forces when the sign of trouble got alarming.
Of course, discipline of a milita was something completely different than a trained army, which again led to early fleeing. Some nations trained their milita better, Sparta for example (yes, even Spartan army was a milita one, only better trained), which gave a huge difference when fought against another milita armies. Early Spartan war against Athens lasted for years, when every year Spartans mustered to siege Athens and burn their crops, but the Athenians refused to surrender due to their superior fleet which continued to feed the city. Only after Sparta built their own fleet of power, were they able to blockade the city and defeat Athens.
Food was the most important aspect of ancient warfare.