there are a number of reasons to think he’s Peter too:

• Hook never fell for women.  If anything he was more interested in war, so the whole Milah storyline is not something he would go for.
• He calls himself Killian Jones and Hook was always proud to be Jas or James, so there’s no reason for an alias unless he’s not James.
• I believe he wasn’t affected by the spell and sent to Storybrooke because of his link to the fairies and their magics.
• He seems to hate himself and what he is—it’s subtle, but it’s there in the way he acts, and the way he was so willing to give in at the end of the fight with Rumple.  Jas never would have given in—IT WOULD JUST BE BAD FORM!
• His hesitance (and obvious annoyance/discomfort) at working with Cora.  Hook was never above allying himself with other villains, but Peter sure would be.
• His knowledge of Neverland.  While Captain Jas Hook knows of it, he was never ever happy to visit the island, whereas Killian was.  You could see it on his face—he was glad to be going home, despite what he’d become.