Ben Levi,
1.) There are plenty of fossils that show “in between” stages between ancient ancestors of modern species and their modern descendants. Although virtually evrey fossil can be classified as “transitional” there are plenty that are clearly so even to one unfamiliar with fossils and evolution.
2.)Before Darwin it was believed that all animals were created on the same day. So if you would ask someone how they would predict the fossil record would look they would predict that all animals would be found together in the different strata ( there should be plenty of “pre Cambrian rabbits”) Evolution predicts that different species lived at different times with new species appearing only in certain eras and not being around before. The fossil record confirms evolution’s predictions.
4.) I don’t think you fully understood what I meant by a nested hierarchy. It is more then “similarities” I explained it more at length in my above comments.