To me, I prefer story 1 because why show us Richard Parker at the beach again if none of that actually happened? What was the point of showing something that didn't happen twice?

Second, why bring up "animals have no souls" and then repeatedly show us that animals do have souls... if story 1 never happened (that the tiger died in the shipwreck)? There is no point of saying "animals have souls" -- if the story is just that Pi killed the cook. What's the profound in that?

So, I choose to believe in story 1. I choose to believe that Pi did make up the second story sarcastically to satisfy the nonbelieving Japanese investigators. After all, he could have said to them, "I survived all by myself." Why tell them he cannibalized the cook? What does it prove? Nothing. So why did Pi have to tell them that story? No reason. If I were Pi and I in fact killed the cook and ate him, I would keep my mouth shut forever! So TELLING story 2 doesn't make sense to me.

Even though story 2 sounds more believable, I think it would make more sense if story 1 was true. If story 1 wasn't true, and Pi indeed was the Tiger himself, why would he tell all these stories about him interacting with the tiger, fighting with him and taming him, if he was the tiger himself? Wouldn't make much sense, unless he was fighting and interacting with himself, and taming himself. For example, the scene where he was on the island sleeping in the trees, he was looking at the boat and saw the tiger looking back at him. If the tiger wasn't real, or he was the tiger himself according to story 2, who was he looking at then?
After all of course, neither story is true because it's a novel :-)