peppersalt.
If I understand you correctly basically you are referring to two things.
1) There is a definite commonality amongst skeletal structures, it is what caused Darwin to come up with his Theory in the first place. For the atheist it points to common descent as the way to explain this. For the believer in G-d creating the world it ‘s “duh we always knew that”.
2) Darwin explains the method of “common descent based on what is crudely described as survival of the fittest” there are many problems with that theory. Not the least of which are the complete lack of a fossil record meaning a record of transitional species such as thousand of giraffes with short necks followed by thousands of giraffes in the next strata with longer neck etc….
I have been to the Museum of Natural History btw and I have read literature on the subject from both pro and con approaches.
The reason actually is because the first thing I ever read on Evolution was from Rav Avigdor Miller and I simply could not believe that Evolution could really be that ridiculous.
So I actually went and read the sources and literature and yes I what I found is that it is really completely utterly ridiculous.