This second part of the season will be very painfull for SF, and from what adam and eddie said before about emma not being prepared to make a choice yet, i see them maybe put CS in the remain on the season and as in more seasons of the show, and in that case neal could even find another person and would be then that emma would see that she wants neal and not hook( I do believe that sf is endgame), but will be very painfull to watch, specially with Cs partying about this. I believe emma will only make a choice in the last season of the show and even on the last episode.
According to Adam, we still have NO idea what is going on in the second part of S3, and Emma not making a choice means not choosing Hook over Neal. It means choosing to be alone. So, there could still be a million reasons why Emma and Hook are filming scenes together. He might be helping her with detective work if Charming is for some reason unavailable (e.g he is cursed with amnesia or is in another realm). Even if Emma has chosen to date Hook for the present, I doubt it would last beyond S3. I also don’t think the writers would keep Emma and Neal apart until the final episode ever. They have too much to work through, talk about, and history to explore. Part of seeing Emma and Neal work through their issues is part of the story that Adam and Eddy want to explore. They said so in the 2×21 official podcast: “How do two people who love each other, but who have so much hurt, come together?” (paraphrase). I believe we’ll see Adam an Eddy give us the answer over the next few seasons. It may take awhile, but I think our wait won’t be in vain. And when it does happen, it’ll be that much more satisfying because then Emma will actually be ready, just as Neal is already ready and waiting for 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