Indeed, how very meta of Hook! Of course Emma and Hook weren’t always meant to be! Why? Because it was fate and destiny (A&E) who brought together SF and meant for them to be together.
It makes me wonder all the more how this whole thing went down, and who (or what alliance of forces) was behind promoting CS and getting rid of Neal. For example, do we know if JMo was on board with CS?
It just seems to me that if you take out Gideon and insert Neal in his place, you get a very different story that makes so much more sense emotionally, especially in view of the “light can only vanquish light” prophecy, and of the name Baelfire — as the comments by @Slurpeez and @Rainbow bring up. Then it would make sense why Henry would be prophesizing — it’d be essentially about his parents.
Insert in there somewhere a plot about Neal trying to save a realm of tortured children from the Black Fairy, and somehow becoming heart controlled by her, and you get a pretty symmetrical story that makes a lot of sense. Then along the way you can probably also explain a lot of Rumple’s bad decisions. This doesn’t even hinge on SF being together in the present — it just hinges on the plot accepting that they have true love. And then the final battle and the scene with Emma sacrificing herself would have been absolutely logical and emotionally quite powerful. I do have a feeling that this might have been the original intention behind the “final battle.”