Well, if we want to be very technical, the Eorzean Alliance would be more of a confederacy rather than a federation of states. A confederation is typically a loose union of sovereign states with very weak central control, with the European Union being the best real-world example.

And, on the point of Ul'dah specifically, my understanding is that Nanamo is no longer pursuing her naive goal of setting up a republic. She has learnt that there are far too many vested interests working against that goal. More importantly, she's beginning to learn to use mercantile objectives to her own benefit. So, yes, don't expect an Ul'dahn Republic any time soon.