While I enjoyed season 3 immensely, some things could've been handled better. My first idea would be that Neverland/Peter Pan is the focus of the entire season and Rumple resumes his Dak One looks fully while there. Then the idea goes as follows:
1. Tinkerbell was the fairy Godmother to Malcom and his family. She served as Young Rumple's mother figure and followed them to Neverland. Malcom forced her to allow the shadow to take Rumple so he could become Pan and stay with him in order to find the Heart of the Truest Believer. Rumple bares a grudge against her for this. They recouncil near the arc's end.
2. Indians show up and Tigerlilly is one of them, not a fairy. Her people are natives from LWM that Pan kidnapped as children, later allowing them to grow up and serve as guards for his camp. They go back to storybrooke with the main cast.
3. Episodes would be used to show Bae's time in Neverland, how he escaped and became Neal Cassidy, Hook's time in Neverland, Pan and Tink together with her powers intact, the Darling children interacting with Hook and others, Rumple kicking ass and being awesome.
4. Pan's shadow speaks more throughout the arc and is the source of his power. Rumple sacrifices himself to destroy it and Pan becomes Malcom again, turning into dust. The Darlings and several natives follow, but are happy in the end. The season ends exactly the same.