Pro: He wanted Emma to have her best chance at finding her family
We as the audience understand this, but do you think 18 year old Emma would understand this? Probably not.
Pinocchio split a long time ago to go gods knows where, no one was really around to explain to her about her destiny. And Neal, being from Enchanted Forest, probably would have been one of the best people to explain it to her since he was from there. But again, he split and allowed August to call the cops on her and get arrested.
Maybe a pro and con list should be done for CS and SF.
Hook
Con: He left Emma in Rumple’s cell to rot.
Neal
Con: Emma has trust issues, partly caused by his actions.
Again, these trust issues go back to Neal. The last time Emma was involved in a crime duo was with Neal and they were a pretty good team (at crime); as Hook pointed out to Emma, they make a really good team but the scars of what Neal did were too deep and she left Hook atop the beanstalk but she let him live.
Hook was hurt that she left him and made sure Emma knew that she hurt him, and if she had trusted him, Hook probably would have helped Emma the princesses defeat Cora instead of hooking up with her.