Sorry, but you’ve already used a common template to explain birds. You can’t use another to explain birds + crocs. Groups within groups is an evolution sort of thing, and your templates can’t be made to fit that. As for the reasons, that originally comes from fossils, and why you think that’s debatable is unclear. Birds and crocodiles are both archosaurs, and archosaurs have a number of clear diagnostic characteristics. There’s also plentiful molecular evidence. While all that could be explained by a template, you’ve already used up your only template in that area.
What you would think is not relevant, since you are unacquainted with the evidence. Here again, both molecular and morphological evidence are clear. Early whales have the central defining character of artiodactyls, the double-pulley astragalus, and notably share a number of SINE insertions with a nested series of artiodactyls, being most closely related to hippos. You could go with a template, but again you would need templates within templates to deal with all the groups within groups. Nested hierarchy, in other words, defeats this template idea.
You might conceivably profit from examining some of the actual evidence and the methods used to analyze it. For birds and crocs, you might in fact start with this: John Harshman: The Phylogeny of Crocodiles, right here on Peaceful Science.