The whole idea of having two stories is that the reader is forced to choose. Throughout the novel Pi explains the similiarities between Science (usually as far as zoology) and religion. Pi says that he doesn't mind athiets (those who choose not to believe) but he hates agnostics. Connecting this thought to the end of the book means that the reader is forced to choose a story that they believe is more true. Choosing the animal story means that you are willing to go on blind faith and believe a good story. Choosing the human story means that you are more realisitc or scientific.
Furthermore, the second story adds depth to the first story, in that it brings to light the horrible things that Pi had to live through, such as killing living creatures to survive. Whether or not you beleive that Richard Parker is a real cat, or represents Pi's will to survive, the truth is that a person on a life boat with no food and water would not (likely) survive on thier own. They either rely on a new side of themselves (and if traumatised create a fractured and separate personality), rely on others, or rely on God.
We mustn't forget that this is a work of metafiction and thus the layers and mutliple endings are very important to creating "a story that will make you believe in god" or in other words a story with a "spark"