Recall, the original ending you get from beating the game for the first time.
When you go to the castle, all of the world leaders from the different time periods step forth, and they're identified as Marle's ancestors and descendants. All of the world's leaders that have ever been have been part of the same family through the ages. (Hard to believe, eh?)
HOWEVER! Here comes the inconsistency!
If you remember, after Zeal's destruction, there is no royal family for anymore!
Consider:
Janus was warped off to 600AD.
Schala ended up in the darkness beyond time.
Queen Zeal assimilated with Lavos.
So who then, propogated the royal family after Zeal's destruction, and the abolishment of its royal family? How was the royal family restored?
Could it possibly be that, Magus, after he returns to Zeal again until to see it destroyed, ends up carrying the torch for the royal family?!
...
No, that couldn't be; the royal family of Guardia already existed when Magus, as Janus, was warped ahead to 600AD.
But, Kino and Ayla from 65million BC were still part of Marle and Guardia's lineage...
...the Zeal family lineage might have actually been a different family lineage than the Guardia family lineage...