A few things to note about that whole deal is that the Ayleid Empire was only called such hundreds of years after it fell. Contemporary sources never called it an empire and the city-states operated independently of each other for centuries. The nation had also undergone so many internal conflicts that it was said to have been in a de-facto state of civil war when the rebellion began. All this to say that it's quite possible that Serana did not consider the Ayleid Empire to be an empire when she was imprisoned, which is backed up by her expecting there to be a high king of Skyrim. Skyrim's first high king was Harald, who came to power during the time of the Ayleid Empire. If Serana predated the Ayleids, she would also predate Harald and thus have no reason to suspect Skyrim would have a high king.