The carnivorous island and why Pi decides to leave. It's more overt in the film but is there in the book; Pi notes that if he had stayed on the island, he and Richard Parker would have died, with full bellies but before their prime, and the island would have eaten them in turn. The question becomes if they would have died too young or if it's a case of We All Die Someday, and Pi would have gotten complacent, refusing to brave the sea again. His braving the sea means he eventually returns to civilization and is able to rebuild his life, but at the cost of losing Richard Parker.
The story itself. Which version is true? The "animal" version (the one we read) or the version where Pi bumps off the Cook and eats his corpse? Anyone reading could argue that, since the agents from the Japanese ministry of transport go "My God" at hearing the second version, maybe the Cook version is what really happened and that the version we read was something Pi (or his mind) came up with means of coping. Or maybe both of the versions are bunk and Pi himself is an Unreliable Narrator.
Hard-to-Adapt Work: The book was considered "unadaptable" because of the strange narrative, but the film pulled it off to rave reviews, albeit by using enough high quality CGI to bankrupt the animation company. The Broadway play has been similarly impressive.
Squick: The descriptions of how the hyena kills the zebra in the book.
Film
Award Snub: Suraj Sharma, who played Pi, did not get nominated for the Oscar for Best Actor. This despite the fact that he practically carried the entire film on his shoulders, acting opposite a green screen to convince audiences that he was staring down a tiger, and starved himself and isolated himself from other people to get into character.
One-Scene Wonder: The Buddhist sailor that comes to comfort the family. He tries to reassure Pi's mother that on the ship, a vegetarian like him counts "gravy" as sauce and not meat, and they can use that loophole. Though the family doesn't try it, they're grateful to him, which makes it more horrifying when in the alternate story, the chef cuts off his leg, waits for him to die, and eats him.
Signature Scene: Richard Parker's Establishing Character Moment, where Pi's father scolds Pi for trying to feed a tiger by hand. To demonstrate why this is a bad idea, he ties a goat next to the tiger's enclosure. Pi's father is right; the tiger kills the goat without hesitation.
Slow-Paced Beginning: Part One of the book details Pi's happy life in Pondicherry, how he took back respect for his name by nicknaming himself "Pi". He also goes on a long introspective journey about religion and how to find God through multiple disciplines, to his older brother's amusement and his parents' bewilderment. Then we get to Part Two, where the story really begins, as the ship the family sails on sinks, and Pi ends up in a lifeboat with wild animals. It's lampshaded in the film, where the author tactfully says that Pi "set the scene" before Pi describes what happened after his family boarded the boat.
They Changed It, Now It Sucks!: Despite the film's good reviews, some have taken issue with how the film portrays Pi's alternate interpretation of events in which the animals were all human passengers of the ship. Specifically, the way the film frames it makes it seem as if this alternate version is the true version of the story, whereas the book is more overt in leaving it as deliberately ambiguous as possible.
. Sweet Dreams Fuel incarnate.