A few things I'd do:
Zoe discovers she's pregnant (she and Wash talked about having children in Heart of Gold
). She names the little boy Leaf, after Wash's "I am a leaf..." speech.
River becomes Serenity's
full-time flight controller. Her psychic abilities enable her to navigate and track better than any machine. She may or may/not develop some chemistry with Jayne. Opposites attrack in the strangest ways...
Book turns out to have been one of many identical copies, replicants of an original template. Each one a "page from the Book". One was a Shepherd, one an Operative, others scattered throughout the 'verse. All of them linked. Don't know why yet, I just like the idea of seeing him again.