How long does it take to make a fossil, and under what conditions are they preserved?
Do we really think we've seen all the evidence? I think only a small percentage of the natural history even exists for us to ponder about... most has been devoured by time and scattered to the winds. I certainly wouldn't assume we've seen it all. We're looking at a very small sample, and always risk coming to the wrong conclusion about where it fits in the big picture.
The author actually addresses your points.