My own personal theory is this:
Tens of thousands of years ago, aliens came and took a whole bunch of animals from our planet, and put them in a giant space zoo. Some humans (or human ancestors) were included in the mix. They were taken away to a giant water world (the aliens were amphibious), where they spent some time being experimented on, and being genetically enhanced. Eventually, some of the human and animal offspring were brought back to Earth, and reintroduced, where due to their genetic enhancements, they were able to outcompete many of the local species, driving them to extinction.
Thus, the ark parable is an ancestral memory of the space ship that took them away (and later returned them); and the flood story is an ancestral memory of the water world on which they were kept.
It makes as much (if not more) sense than what Christians actually claim happened
ETA: Dammit...I've just created the basis for a whole new religion! L. Ron move over!