I think there are two questions that come up with this turn of events:
1) When they say “villains” and “heroes,” whose POV is it? Do they all agree on who the villains/heroes are? Are Rumple and Isaac on the same page, so to speak? For example, what happens to Hook?
Similarly, does the author write something like “and all the villains had their happy endings,” or does he have to write more specifically what happened?
2) What’s in it for Isaac? So he first went with Regina, realized that she wouldn’t use his abilities — she’d do “nothing” as she said — and then at that point skipped back to Rumple. Technically, that scene where Rumple is focusing on the inkwell gave me the impression that without the author’s intervention Rump was essentially a goner. I think the author wrote him back into consciousness with his line “where Rumplestiltskin waits.” What gives?
Is the author simply after a better story, or does he have other motivations beside this? Is he, much like Rumple, addicted to his power?