Are you a lumper or a splitter?

[Anomalocaris]

I think focusing on the similarity helps in reconstructing the evolutionary history of adaptations, enabling us to develop explanations for them.  It is these adaptations in their most extreme form that we identify as differences, so in order to understand those differences, we need to focus on the similarities.

Differences and similarities are complementary. Focusing on genetic similarities enables the reconstruction of the common ancestors of two different organisms. But focusing genetic differences enables the determination of how long ago the last common ancestor for the two organisms lived.

What is more, to understand what drove adaptation and evolution, that requires a focus on the differences, not the similarities.

So Evolutionary history can not be completely understood without either.

What to focus on depends on what the objective is.