How did Noah get Kangaroos to Australia?
Short of calling the entire Geology and Paleontology communities a group of liars, you'll be hard-pressed to make the case that we find the same fauna throughout these superpositioned layers. Furthermore, your use of the word Phylum leaves your argument a bit vague and overbroad and may confuse readers, as they may not be aware that "Phylum" is an extremely generic classification system, since everything from humans to the most primitive fish (along with every other vertebrate; like birds, reptiles, amphibians, etc) belong to the Phylum of Chordata. So technically your statement is true, since the primitive fish of the Cambrian fall into the same exact Phylum as we do. However, this does nothing to change the fact that we find a gradation of different Chordates as we move up the layers. Readers who are not familiar with the meaning of "Phylum" may think you are making the argument that we indeed find modern mammals and reptiles in Cambrian, Ordivivian, Silaurian and all the other ancient layers where the only vertebrates we find are still primitive fish.
Within the Pre-Cambrian, the Vendian layers clearly contain a limited number of primitive animals. So far, Profiera (sponges) have been discovered in this layer, as well as a number of other primitive orders. Dickinsonia, Cyclomedusa, Eoporpita, Arkarua, Kimberella are a few examples of Vendian layer creatures with semblance to modern day counterparts, yet sometimes difficult to categorize due to anatomical differences. It is clear that we find more than just microbes in the layers preceding Chordates.
I am unaware that anyone has ever proposed the idea that flying squirrels were ancestral to bats. There is no reason modern flying squirrels should possess the exact characteristics between bats and their ancestors as they are contemporaneous to one another. Generally when Creationists refer to transitional forms they are referring to fossils that "should" contain the intermediate steps between two types of animals. Such transitions have indeed been recovered. In addition to the examples I gave in my opening statement, I would also like to refer to Acanthostega and Ichthyostega, as they provide excellent examples of the transition from fish to amphibians. They are found in the upper Devonian; well 'above' the layers we first start finding fish and well before the layers we start finding amphibians and reptiles.
There are a number of Paleontological facts that disqualify a worldwide flood as the cause of fossil placement. First there is no reason that a flood should bury marine animals as they should be most likely to survive a flood given that they are already suited for living in water and it seems unlikely that the existence of more water would not only cause their deaths, but do so before animals not suited for an aquatic life.
There is also the task of explaining how and why Noah's ark would have been able to leave the animals in the various continents. Because we only find Kangaroos (and their fossils) and other large Marsupials in Australia, one would have a hard time explaining how and why this is the case in the context of a worldwide flood and an ark that preserved a few animals. On the other hand, it makes perfect sense if these animals share a common ancestry with their placental relatives whom they were isolated from due to the shifting of continents, and fulfilled parallel niches within Australia via speciation. Unlike the flood/ark conjecture, faunal succession/common ancestry along with continental drift explains why we find fossilized lions (even larger than contemporary African lions) here in Los Angeles.
Furthermore, there is no reason why Komodo Dragons, Elephants, Rhinoceroses, Tigers, Seals, and Peacocks should have survived the flood, while Mosasaurs, Mammoths, Tricerotops, Velociraptors, Ambulecetus, and Archaeopteryxes didn't. Not only is there no reason for a flood to wipe our sea dwelling creatures, but they themselves should not exist in the sequence they do. If a flood is somehow responsible for the destruction of sea life, there is no reason whales should only exist in the upper layers (starting with the Palogene), when we find rudimentary variations of fish (as opposed to modern fish) as low as the Cambrian. In addition to the wide berth between whales and ancient fish, we find plenty of land dwelling vertebrates in between the two, in addition to animal burrows (meaning the deposits must have happened over time).
If the flood is responsible for the extinction of certain birds, then you have to explain how flightless birds like Dodos and Ostriches survived the same.If a flood happened today, it would not bury life in the same order as Evolutionary Theory. Furthermore, we would find remnants of human civilization buried and mixed along the same layers as everything else, not merely in the upper layers. Given that reptiles and amphibians tend to be well-adapted to water, we would find them in layers above many if not most of the mammals, since many mammals are simply not accustomed to water. Fish would be the most successful given the fact that their environment would only becoming larger. Arthropods not suited for water, such as Scorpions and Praying Mantises would not survive such a flood.
The flood and ark explanation provides nothing more than a series of ad hoc explanations for the placement of fossils, and requires even more ad hoc explanations for the various discrepancies and contradictions it creates.
