Good lord, Tom Bombadil is the last person you should center a movie around. He was always meant to be a cypher. Yes, the mystery around him is intriguing, and the theories are all interesting, but actually pinning down his story I feel will only diminish him. He's in the story for two reasons, to give a little whimsy before things get really dark and serious, and to show that the world is much larger than what is shown. Sometimes side characters are just meant to be side characters. If they feel the need to do more Middle Earth stories, do some more stuff from the Silmarillon, or grow a pair and do an original story.