He should be the Mayor but he did not remember about that, like rest of the folks. And after he find out, he died couple hours after. That's why Regina was still the mayor.
EDIT: Besides the second Storybrooke existed as a whole. Only Granny's Diner was taken out from Storybrooek to Camelot and back, from Camelot to Storybrooke. Hook just cast the curse. He did not recreate a whole town for the third time, That's why Snow should be the mayor since she cast a curse. She just gave up that position to Regina.