The side stories are among the strengths (and weaknesses) of the novel. Here are my choices for best and worst side stories.
Best:

1. The Bocchiccio Family and how they helped bring Michael back from Sicily. This could have been a novella in its own right.
2. Neri, his background, and how he came into the Corleone Family. Another novella—perhaps a movie if fleshed out.
3. Luca Brasi’s background, as told to Michael by Filomena. Scary.
4. Vito’s rise and the gang war that he won (including how Luca handled the Capone gunmen).
5. Sonny and the boiler repairmen.

Worst:
1. Jules, Lucy and her operation. Puzo put us through an agonizingly boring and sappy interlude just so he could describe an operation that, probably, some friend or relative had, and that he couldn’t resist describing.
2. Everything about Nino.
3. All of Johnny Fontaine after Connie’s wedding.
4. Every bit of the Hollywood BS Puzo burdened us with. That Hollywood BS was what ruined “Last Don.”
Your views?