Five Kingdoms 1. Fungi - Fungi 5. Divisions should be monophyletic, the Five Kingdom scheme is not. Separating Plants, Fungi and Animals from the Protista makes Protista NOT monophyletic, they share their common ancestor with Plants, Fungi and Animals. So, either reduce the number of Kingdoms to Prokaryote vs. Eukaryote, or increase the number of Kingdoms so that each Kingdom is monophyletic.
Kingdoms really become a division of convenience.
Protozoa were classified by how they feed and how they move. Artificial, cause assumes things can not reverse - assumes all traits are descendent. Different reproductive stratagies Differ also in carbohydrate food reserve, number of flagella, cell wall components and habitat. Some characters and sequences are considered more appropriate than others for use in constructing these trees. How much time is not clear, since we can not always say how fast certain changes have occured.