That sense of familiarity when Emma walks into Neal’s apartment..I think it’s a direct contrast to that fact that she didn’t feel any sort of recognition with Hook in 3×11. There was nothing there between them. But with Neal, even just his things, it’s instantaneous.
Some people say there is this connection between Hook and Emma, but personally, I think there is a much deeper, intuitive understanding between Emma and Neal. They both were lost children who found each other in an otherwise lonely world. They were thieves together. They found a home in one another. Both Neal and Emma dreamt of their parents coming for them, and both lived sad existences on their own until they met. Emma is always saying things like, “Neal taught me that.” In 3×4, all Emma had to do was see tally marks on a cave wall to know that he’d stopped counting when he’d given up hope of getting out of NL. Hook then tried to redirect the attention to himself by using line that he knew what it meant to lose hope too, and Emma totally called him out on it saying she knew what he was doing. It’s just too forced with Hook. Yet, with Neal, things come naturally, like they’re second nature to her.
"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