I don’t feel the writers “have” to do anything but tell a good story and we all have different ideas of what that means. I’m sure Hook’s backstory is going to be everything needed to keep Hookers happy, by showing new layers and depth. I also think they’re going to continue to give us reasons to root for Neal to get back to Emma. Beyond that, I hesitate to make big predictions right now about what will happen when he does.
I still am rooting for Neal and Emma to work it out. The writers placed clues that Emma loves Neal in things like Emma keeping the yellow car, something so symbolically Emma that it was part of her brief OUAT:WL stunt double cameo. A sheriff’s car might have established the timeline better. Then they gave Emma Bae’s sword.
The writers are not preparing the audience to think as badly of Hook or Neal as some fans do so I am not sure what they have in mind. Maybe Hook or Neal have to go through heartbreak at Emma’s hands in order to come to grips with what happened in the past. Maybe it helps Neal or Hook understand how Rumple could have killed Milah, what type of despair drives a person to that. NL is all about facing the past, so as these characters get through this story arc I do expect a lot of changes in what I think will make them happy, but I do think the writers will want them to be on the road to that happiness.
Edit : Yes, 100% agree with Heather and Phee — Neal is not just a flat cardboard obstacles in the way of a ship (for that, see Tamara).
“If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn't. And contrary wise, what is, it wouldn't be. And what it wouldn't be, it would. You see?” -- Lewis Carroll, Alice's Adventures in Wonderland & Through the Looking-Glass