I think that Emma and Hook will end up together in Storybrooke. When she does get back, I’m thinking she’ll find Neal, and she’ll be rather upset with him. Also I’m thinking that she’ll find August/Pinocchio and she’s REALLY going to be upset with him. She’s emotional and confused and who better to comfort her than the ever so gorgeous Hook, who she’s spent SO much personal time with.
The most important thing is that Hook gets her, she didn’t have to open up to him for Hook to understand her.