Why do you think Emma is having such a hard time telling people like Snow and Charming (and even Hook) that she doesn't want to be with Neal again? For instance, when Neal asked her out on a "date", she didn't say she wasn't going to go, even though she never showed up. At the same time, she allowed herself to be convinced by Charming to give it a shot. Was she still feeling confused about Neal and not sure of how much she cared for Hook until the Tink/jealousy scene?
Because she’s Emma. She has an incredibly hard time expressing her deepest feelings, she doesn’t want to go into revealing what Neal did to her with her parents and everyone else because that would entail being vulnerable, she doesn’t want to waste time talking about herself when Henry’s still in danger and she has a sense that something’s not right, and because she doesn’t want to hurt anybody. For all her armor and badassery and toughness, Emma is an EXTREMELY empathetic person who really doesn’t like causing other people pain. She didn’t want to HAVE to tell Neal that she wanted him dead; who really WANTS to tell that to someone they care for and their first love/father of their child? But because they were in the Echo Caves, she had to and so she did. At no point has she ever acted or said in any way that implies she doesn’t know how she feels for Neal: she is very clear on how she feels for him. She loves him, probably always will, and has less than no desire to be in a relationship with him again. But because her dynamic with Neal has always been that of the powerless 17-year-old who did what he said and let him control her, because her parents are pressuring her, and because she’s confused about what she feels for HOOK (not Neal), that means she’s trying to just avoid the subject as much as possible.
Neal gave her an ultimatum at the diner scene — kind of a cute/adorably awkward one, but an ultimatum nonetheless. Show up for lunch with me, or I’ll quit pursuing you for good. Even if Emma HAD had some desire to get back with him, that puts all the pressure on her to GO MEET HIM FOR LUNCH TOMORROW OR OMG HE WILL LEAVE ME AGAIN. And clearly she’s not ready to deal with him at all and doesn’t want to get back together, so she doesn’t go. She had no idea that Charming was going to show up and try to shanghai her into it. As far as she knew, by not going she was serving notice to Neal to stop pursuing her, and hoping that this time he’d finally take the damn hint. (She was at the docks, clearly looking for Hook, while he was at the diner where she was supposed to be. My heart.) Then we don’t know what would have happened if Blue hadn’t been attacked. She would have gotten to the diner and seen Hook drunk and completely miserable, and you can bet that would have been her priority over a lunch with Neal she still didn’t want to go to. (Seeing as she had to take the time, while Blue was screaming, to find out if Hook and Tink had been knocking boots on the sly).
Hmm. Suddenly I need an AU/fic of this. For reasons.