1. One of the traditional arguments for evolution is anatomical similarities between organisms. A more recent argument is genetic similarities between organisms.
But one question is whether these are two independent lines of evidence. To the extent that anatomical similarities are the result of similar genes, you have a cause/effect relationship between genetic similarities and anatomical similarities. Indeed, this suggests the appeal is circular. Organisms are anatomically similar because they are genetically similar.
I recently said, What's the relationship between greater similarity and sharing more of the same genes? How does genetic affinity and resultant similarity imply evolutionary genealogy? Isn't Singer's inference circular? In such comparisons, you select organisms that have the most in common. Similarity is your selection-criterion. So, by definition, you group organisms according to degrees of similarity or dissimilarity. But the way you arrange them doesn't imply that that's how they developed. Rather, the hierarchy of ascending commonalities is the result of what you selected for. So that relationship is imposed rather than discovered.
Take a bag of colored marbles that range along the spectrum. I can rearrange the random assortment according to any two marbles that are shades of the same color. The color of one marble is more like or less like the color of another marble. Some marbles are nearest in color, some are farthest, some are in-between. Some range along one side of spectrum, some along the other side. It's not the marbles that single out that particular arrangement, but what I'm looking for.
Let's expand on that by taking another comparison. In traditional painting, red, yellow, and blue are primary colors while green and orange are secondary colors. You produce green by mixing blue and yellow. You produce orange by mixing red and yellow.
Two shades of green are alike because they share the same or similar amounts of blue and yellow. Lighter green has a higher percentage of yellow and lower percentage of blue. Darker green has a lower percentage of yellow and higher percentage of blue. So two shades of green are more alike or less alike depending on the amount of yellow and green they posses.
That's analogous to organisms that are more similar or dissimilar depending on similar or dissimilar genes.
However, while that's consistent with evolution, it doesn't imply evolution. To continue with my analogy, a painter mixes colors for variety. What if God likes variety?
2. A Darwinian might object that that's ad hoc. But actually it goes back to the ancient principle of plenitude. That's a theologically respectable rationale that long antedates Darwinism. So it wasn't concocted to deflect Darwinism.
There are, moreover, other explanations for similarity. Why do sharks and dolphins have the same torpedo shape? Because that's an efficient shape for their natural element.
Why do humans and monkeys have forward facing eyes? Because they share a common evolutionary ancestor?
One explanation for forward-facing eyes is that predators need binocular vision. But are fruit-eating monkeys predators?
Another explanation might be that humans need binocular vision for eye/hand coordination. We'd be unable to take full advantage of our hands, with the opposable thumb and fine-motor control, if we had eyes on the side of the head.
3. It might be objected that I've oversimplified the argument. To the extent that the fossil record is chronological, there's a developmental pattern.
However, that's difficult to assess. Common ancestry, per se, does not imply macroevolution. For instance, dogs have a common ancestor in wolves. That's consistent with evolution, but that's consistent with the falsity of evolution.
Are fossil "hominids" ancestral to man, or just extinct apes?
It can be misleading to judge what animals are good at from their anatomy. For instance, goats are surprisingly good tree climbers. They climb fruit trees. On the face of it, goats are poorly designed to climb trees.
Likewise, snakes don't seem to be well designed to climb trees, yet they do so with ease. If we didn't know from experience that snakes were good tree-climbers, could we tell from fossilized snake skeletons? Same thing with goats.
4. It also depends on possible alternatives. Consider old-earth creationism. Suppose God phases in life on earth. Introduces different natural kinds at different stages of natural history. If we view the fossil record with that reference frame, is it consistent with fiat creation?
Perhaps a Darwinian would object that that's ad hoc. But is it?
Suppose dinosaurs aren't compatible with modern mammals. They require a different climate. Moreover, the dominance of dinosaurs is antithetical to the dominance of mammals, or vice versa. If they can't coexist, then they can only exist in sequential epochs, allowing for some transitional overlap.
Young-earthers have their own explanation, based on the disruptive effects of a global flood.
If, moreover, incremental evolution just doesn't have the internal resources to account for the origin of life, or bridge over incompatible body plans, then that invites theistic alternatives.