Herodotus was a great narrator. Reading his books is really entertaining, and he manages to simply estate things and give quite a good deal information without it becoming a burden. He has some agenda, but I find him more trustworthy than Ktesias, for example!
What I have gathered from him and other sources, for the time being, is that, as Pierre suggested--and until I can read Briant's book to get a more Persian POV--, the Ionian state-cities were indeed very powerful by themselves, probably more powerful than the Western Hellás cities (not in Italy and Sicily, I mean the Continental, Balkanic cities).
Authors suggest that Ionians were less powerful than mainstream, Hellenic cities like Athens, Corinths, Megara... because they didn't have so many colonies, which indicates a lower growth rate.
But the truth is that most Ionian--and Cycladic--cities enjoyed better fields and crops, most of them grown on aluvial planes of the water rich Ionian rivers, which dragged lots of minerals from the mountains after defrost and rains, and could sustain bigger populations before engaging the colonization resource to keep the population under control. We then have a handful of cities (traditionally around 12, but it fluctuates with time) in the Asia Minor coast, and then several important islands (the most prominent were, probably, Naxos and Chios, although Samos , Lemnos and Lesbos were very important as well) with big cities, large forests and important naval power.
Bigger population means bigger hoplite-class citizens, which means they could field larger armies if need arouse. The fact that Athens, as metropolis of Miletos, was able to send 20 trirremes, which was half her navy at the moment--they were about to have trouble with Egina, and decided it was wise to keep something for themselves--, is very significative. Athens only managed her huge navy the next decade after getting hold of important silver mines which were put to massive ship construction by the leading democratic party of the moment. Eretria--not exactly a big state-city, it's truth--could just send in five ships. That was probably a big war effort from the most impotant Euboean city.
As a comparison, just four years later, Chios sent 100 trirremes to the Battle of Lade, and they probably had several more to defend the town while the fleet was out. Each ship was sent with a compliment of 40 hoplites (or epibatai, which are a kind of Marines which could work both at naval battles or to form a phalanx on the ground) instead of the usual 10 in later, Delian League times. Samos sent 60 trirremes, Mytilene sent 70, and gave 8 more to Histriaios, Aristagoras's father, who became a Hellespont pirate.
The total war navy the Ionians could gather to the battle of Lade--which is, by necessity, lower than the total available at the moment, and the quid is in assessing how much smaller than the full navy it was--was composed of 353 trirremes, full of fighters.
An equivalent fleet gathered at the time in the Continent would have seen Athens 40 ships, Eritrea 5-10, Corinth probably was the most powerful navy at the time (let's suppose double the Athenian, 80), and not many more cities would have had big navies, their war bussinesses mostly conducted by land troops...
So the Ionians were powerful, prosperous, and conducted their bussiness with success, even under Persian rule, until they lost access to the enporion in Naukratis, after Great King Cambyses II took over Egypt ca. 525-4. The decreased revenue from such an important market must have been a strong blow to the Ionian cities, and it may have threatened their ability to keep their high life-style and paying their taxes to the satraps.
My thinking goes in the following direction: while the cities in the Panionion (the Dodekapolis) were able to get together a big hoplite army, they weren't as motivated to do so until the Athenians arrived in Ephesos. After the sack of Sardes, and the Battle of Ephesos, the Ionian, Karian, etc cities were pretty busy defending themselves from the Persian army which was striking the rebel cities in many simultaneous fronts, and the possibility of a big, grand, final land battle was denied because they could not move their land armies to get together. Therefore a naval battle was proposed, which the Persians, probably led by Prince Datis (of Marathon fame) after recovering the insurrect territories on Chiprus and Karia, didn't fail to accept.
What's for sure is that they were able to put up a good fight, and that's probably why the Great King Darius the Great decided to create a "buffer zone" between the Western and Eastern yaunâ, a sent Datis and Artaphrenes Jr. to take over the Cyclades and Euboea. i think Marathon was just a 'plan B' to get Hyspias back into the power in Athens, but that it was far from being the main goal of the expedition.
But we will discuss that later on... :)
As Samhain approaches, and the weather is foul, Nanowrimo is closer and I am eager to start writing (even when I haven't yet been able to find suitable names for my Persian main characters!). With the Sun and the leaves Fall, we will enter into a darker period, the Season of the Chrone, a time of inner reflection, deep mysteries, magic and shadows, ideal for staying home writing... :-)