While it is not much, the little things add up. Emma was afraid that being the savior meant no day off. She just had a year off! Neal knew that they would see each other again. He had hope, which Emma needed. She did not want to leave and I agree she was already teary-eyed and upset before Hook approached her, so a lot of emotion carried over. She still had not rejected him at this point so what else could she say? Emma never had time to sort through what she feels.
They do add up which is why I believe Neal will always best fit Emma’s dream of a home-life and family. True, Emma got a year off, but she also didn’t have her newfound memories of Neal post-curse of Hook to evaluate how she feels. For her, it will have only been like a day when she regains her true memories. Nevertheless, her fake memories will give her some perspective about the life she wishes for her and Henry: a normal life together without magic or constant threats. It all comes back to which man’s dream line up with Emma’s dream.
When magic comes in, these painful things are going to happen, and Neal crossed worlds to be with Emma. I have no idea why he is not the one to go find her in NY but the writers better have a GOOD explanation why.
From a narrative perspective, I think there is a reason to the madness of it being Hook instead of Neal. The writers have to set up a contrast. Hook represents adventure, danger and otherworldliness while Neal represents the less flashy, but still brave-hearted, kind man who fits Emma like a glove. Yet, by bringing Hook to NYC instead of Neal, the writers are making Hook a fish out of water, making it painfully obvious that Hook doesn’t belong in this world. Hook is running around the big city dressed as a pirate waving his hook around making him look like an escaped convict from a mental institution. No wonder Emma probably calls the cops on him! Hook doesn’t belong in Emma’s world of NYC with her. Instead, he’s been sent to call her back to the world of fantasy and make-believe. Hook might represent adventure to Emma, but he also represents danger to the life she’s built for herself and Henry. By calling Emma back to SB or EF, Hook is asking Emma once again to put on her armor as the savior, to risk her life and Henry’s, for the sake of her family. For all we know, not only are Emma’s parents in jeopardy but so could Neal be in danger! Perhaps Neal sent Hook as a last recourse, or because he believes Emma favors Hook, but the point is, Hook sticks out like a sore thumb and doesn’t jive with Emma’s current happy abode or chosen lifestyle.
By contrast, Neal is the lost boy to Emma’s lost girl who, like her is from another world but called this one home once. He knows this world like she does and feels more comfortable in A Land Without Magic due to magic destroying his family once. Emma and Neal are end-game though, so the idea of Neal, Emma and Henry settling down together is Emma’s idea of a happy ending. She got a taste of that this past year. Taking a year off to raise her son has probably caused her to realize that her idea of a happy ending simply is having a good life in NYC with her son. And who best fits that mold? It’s Neal! He was independently living in NYC with a job and an apartment. It’d make the most sense for Neal to wind up back in the city with Emma and Henry as their everyday happily ever after scenario. We had a glimpse of Emma waking up at 8:15 to the same song “Charley’s Girl” that Neal was listening to back in 2×1! This shows pretty conclusively that both Emma and Neal share the same tastes, dream and hope, which is simply to have a good, normal, and honest family life together. Their dream is so simple when compared to the pirate escapades that Hook probably envisions for himself and Emma on the high seas. Hook will always have the sea in the blood. By contrast, all Neal wants is to build a home with Emma and Henry.
"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy