I just figured out how to fix 3B.
First of all, Hook needed to die in 3A. Thematically, it was his time.
Then, in “Quiet Minds,” Belle, not Neal, should have used the Key. But, instead of killing her and resurrecting Rumpel, it makes her the new Dark One — and the donor of the brains for Zelena’s time-travel spell. This also marks the beginning of Dark One Clippy. Zelena captures both of them.
Taking the place of “The Jolly Roger” is an episode where, while imprisoned, Belle and Neal find a book (of Cora’s? Maybe Lumière tells them?) about Wonderland and learn that it has a White Rabbit who can create portals to other lands. They also begin to wonder why Zelena hasn’t turned him into a flying monkey. Then, it becomes clear: She has a backup plan involving him. At dinner, she cursed his lips to remove Emma’s magic. This, naturally, leaves him anxious about kissing Emma during the present-day plot, even after she regains her memories.
At the end of “A Curious Thing,” when Zelena returns from messing the Curse, Neal freaks out, because he and Belle had found another way. Zelena says “Oops!” and drinks her memory-preservation potion. Then, she commands Belle to drink one, too. After a fight with a monkey (Phillip?), Neal wrestles it from her and leaps through a looking glass to Wonderland. But Zelena’s not too concerned, because of Walsh.
In “New York City Serenade,” because Neal showed up instead of Hook, things play out differently. He actually likes Walsh. He even mentions how he too was engaged until about a year ago. When Emma asks what happened, Neal explains, “Well, once she shot me, I knew it wasn’t gonna work out.” He’s also curious as to how Emma arrived at the name Henry. And she admits she’s not quite sure. He rebonds with Henry, who gets a strange sense of déjà vu. Then, everything changes, when a monkey attacks! Because Zelena has just been made aware that Neal managed to get away with the potion. Once he’s taken care of, Emma asks Neal for “that potion.”
Interestingly, this ultimately changes a bit of dynamic of the finale. Instead of Emma debating telling Rumpel what happens in the future, it’s Neal who does struggles with this. Rumpel tries just keeping them in the past, but Neal convinces him otherwise, using logic he gained from watching BttF. And, somehow, that stinking’ urn still manages to go back with them.
And Imagine the possibilities for S4! How Belle looking into the Trolden Glass could trigger the same thing that started happing to Rumpel in that season. And imagine the possibilities for Belle and Dark One Clippy! I know you're already thinking it, Rumbellers! But, who would banish her from town? Moe? Moe. Definitely, Moe. I’m also fine with changing the Marian storyline from S4, and leaving Will out. Of course, 5B would be VERY different!
That. Last. Paragraph. Was originally in the tags. They got cut off. Who knew there was a limit!? I may have missed some things that I had. Another thing in the tags was that Zelena would have been found out earlier, and they’d know what happened to Belle.