Except for Miletus, which was sacked as an initiator of the revolt, the other cities were treated rather reasonably, going as far as recommendations for the settled Persians to respect local religious traditions (Herodotus VI 42-45).
This does not necessarily need to be seen only as a reasonable conquering policy, but also as a diplomatic and political approach: once Darius asked for the submissions of mainland Greek cities, many of them accepted, based on the previous behavior of the conquerors in Ionic cities. Athens and Sparta obviously remained aside, but this was also because they were also assuming a regional power status and would not find it calculable to surrender without a fight.
Reasonably enough, though, the Persian invasion could also be seen as a direct consequence in the involvement of the Athenians in the revolt of the Ionic cities and in their attempt to preserve a democracy here and consolidate a united front against the Persian invader.
Despite all these positive aspects for the Persian Empire at the moment of the war, the invasion itself failed because of several reasons. First of all, despite its excellent administrative system, the empire was already overextended and invading a foreign country, far away from the main basis of operations in the heart of the Persian Empire, would make it difficult to supply and replace the number of fallen warriors.
Herodotus is not a reliable source in matters of the number of invading Persians (his figures go well into the couple of thousands), but one could assume that the army numbered at least several tens of thousands. These needed to be supplied and fed in a country often hostile or, at least, in a land such as Attica that did not offer so much feeding possibilities. The land was also unknown, while the defending Greek armies could make use of every part of the landscape in order to find the best allies in the nature (the best example is probably given by the stand of the Spartans at Thermopylae, which allowed a very small army to stand up to the Persian army exactly because the terrain was difficult and the mountains protected the flanks).
At the same time, an important element in the Persian defeat was also the fact that the Spartans and Athenians realized the danger that the Persians represented for each of their individual freedoms and were able to put aside their differences and join forces in order to fight together. Their identification with a common Greek spirit made this possible and represented an essential asset in fighting an army that was formed of many foreigners with less of a will to fight.
It is true, however, that Darius underestimated his opponents, compared to some of his other campaigns and, as such, the preparedness of the army lacked the rigorousness of some of his other wars. He had not taken the time to study his opponents and, encouraged by his victories against the Greeks of Asia Minor, assumed that the task would be easily accomplished.
The source used to describe the Greek - Persian Wars is Herodotus. The reliability of this source is questionable at times, but this is generally with regards to some of the concrete facts with which modern historians are used. For example, he puts the Persian army in the hundreds of thousands, when it probably never surpassed several tens of thousands. Some of his numerical exaggerations bear a mythological aura from time to time, as do some of the other descriptions with which he seeks to turn his historical work into a more literary one.
Nevertheless, Herodotus is always very detailed and keen in developing the political elements and reasons that lead to some action or other. He describes in great detail the political situation in the region and, indeed, only begins writing about the Greek-Persian War in the 5th book. He is very rigorous in describing factual details of the society and political scene, which is probably not something easy to do in the Antiquity, especially since facts themselves, while being gathered, usually used to have a mythological explanation.
One should also consider Herodotus writings from the perspective of being the only available writings describing a historical event taking place 2,500 years before our present day.