Scientific theories are in principle subject to underdetermination in that multiple theories could account for the data. In the natural sciences this possibility is strongly resisted. When Darwin proposed his theory in 1859, he could not show that a version of special creation would not account for the data. What he and Huxley did instead was to advance a new definition of science that was completely naturalistic so that special creation was no longer science, no matter what evidence it might have in its favor.
The late 19th century also showed the rise of agnosticism and secularism, which are tied to the new definition of science. William Dembski has a chapter on this in his book Intelligent Design, The Bridge Between Science & Theology (Chapter 3 on the Demise of British Natural Theology). Dembski is right to call naturalism idolatry.
Darwin’s strategy won the day so that few people now are even aware of the older definition of science that allowed special creation. One could say that creationists and intelligent design advocates have this in common: both reject the naturalistic definition of science. In that sense both want to return to a former definition of science, though it is not being stated as a return but as a better definition. Perhaps that reflects the anti-historical bias of our day — who cares about the past that has been superseded?
One could argue that the 19th century naturalistic and positivistic turn was a result of Enlightenment thinking in the 18th century. And one could argue that Enlightenment thinking arose as a result of mechanistic thinking in the 17th century. And one could even argue that that was a result of the nominalism that arose in the late medieval and renaissance periods. But even so there has been much continuity throughout this time of what natural science is.
Is it better to promote a post-naturalistic, post-secular science or focus on critiquing the mistakes of the past? Both are worth doing, though the latter has been neglected. Several points could be made by those who accept a form of special creation: (1) they are not scientific newcomers or rebels; (2) they are in continuity with a long past; (3) their opponents have broken from the historic mainstream of science.