What is the meaning of 'state of nature' in On the Origin of species by Charles Darwin?
I would think that by "state of nature", he probably referred to any non-cultivated species. As @David suggested in the comments, the expression "in the wild" could also be a good replacement for "in a state of nature".

I think that the first paragraph you quote could be rephrased in the short sentence


  There is more phenotypic variation in cultivated species than in non-cultivated species.


My sentence is more concise but of course, is quite a bit less pleasant to read. Darwin was a very good writer after all.