As Secord explains, Darwin's observations led not to scientific conclusions but religious concerns:
The different varieties of tortoises and mockingbirds provided powerful evidence of the relations between the Galapagos fauna and that of nearby South America. In geographical space, as in geologic time, closely allied species emerged successively and in order, just as they did in the fossil record. These relations, which impressed Darwin throughout the voyage, suggested that species were not specially created.
Let's see now, where's that verse in Genesis about birds on islands being completely different than those on the nearest mainland? Oh well, in any case Darwin argued powerfully that special creation must be false. The evidence for evolution was weak at best, but it had to be true. Religion drives science and it matters.