Playing as Isabella of Rome, I just moved from Antiquity into the Exploration Age. I am playing on the YnAMP world map. I only had two cities in Antiquity, my capital of Roma and one city I settled on the Iberian Peninsula. Besides Rome, this Iberian city is by far my most populous settlement. Since I am playing Isabella and planned to choose Spain during the Exploration Age, I basically set up this second city as my new capital of Madrid.
But, when I did transition between ages, only a small mining town without coastal access was offered as my new capital. I am annoyed and confused. Neither size, nor city status, nor coastal access appears to matter.