Disclaimer: If you haven't seen the movie yet, please don't read this answer.
I know there are people who like to believe the animal story. I did too, but when talking about it with someone else, I realized it's just our human side that makes us want to believe it. We don't like the other being true because it's so sad and dramatic. But as much as I loved the story with the animals, it's just a metaphor for what actually happened. Life of Pi is not a fantasy movie, it's drama, it's a dramatic story.
His animal story is what his mind likes/chooses to believe over such a dramatic event that is losing his mother in a violent way and a shipwreck.
The story he tells in the end is the real one, and even if it's not said clearly, we know that's what actually happened. He just elaborated that and invented the animal one to get over it. It's psychology, after all.
Think about it: when in the end he asks the writer "what story do you prefer?", the writer chooses the animal one. Perhaps because it's more interesting or less dramatic/strong, but certainly not because the writer believes the story is real. Pi knows the story is not true, and he knows his mother died in that lifeboat. He took revenge and did desperate things in a desperate situation.
There are actually some proofs to this: when seeing the movie, didn't you wonder how come the tiger didn't come out of the covered bit earlier? Why didn't the tiger fight the hyena under that tarpaulin? She came from there, so they must have... co-existed there, if it was true. The answer is simple: there was no tiger, there was no hyena, orangutan or zebra
The tiger comes out suddenly because... Pi's evil side comes out suddenly. It "didn't exist before". And we all know a tiger can't come out from nothing.
Another proof is the human-shaped island, where trees are edible, but that at night, being it so welcoming, "turns into" acid lakes and killing trees.