But cases of great difficulty, which I will not here enumerate, sometimesoccur in deciding whether or not to rank one form as a variety of another, even when they are closely connected by intermediate links; nor will the commonly-assumed hybrid nature of the intermediate links always remove the difficulty. In very many cases, however, one form is ranked as a variety of another, not because the intermediate links have actually been found, but because analogy leads the observer to suppose either that they do now somewhere exist, or may formerly have existed; and here a wide door for the entry of doubt and conjecture is opened.
Darwin seems to have hit the nail on the head, here - this is where much creationist attack appears to stem from. They see all the evidence, but then say "but you're just guessing at the intermediate forms". Of course, we can nowadays compare DNA and the like, which (again) Darwin would have been most glad to have had. However, he goes on, in an effort to allay the problem raised by his last sentence:
Hence, in determining whether a form should be ranked as a species or a variety, the opinion of naturalists having sound judgement and wide experience seems the only guide to follow. We must, however, in many cases, decide y a majority of naturalists, for few well-marked and well-known varieties can be named which have not been ranked as species by at least some competent judges.
So...let's have a vote? Perhaps before the advent of being able to use DNA to place an organism on the tree of life by comparing its sequences to others already catalogued, this was indeed the best way. I suppose, in a way, the current strategy is also a majority vote - the majority of biologists agree that this method works as well as, or, in fact, better than, a rather subjective appraisal by a committee of naturalists.