The answer, of course, is that nature's design is just one dimension of theology. Suffering results from the curse occurring subsequent to creation. The cure for sin, through redemption alone, shows the Lord's eternal perfection in the greatest way possible. A second attack on Paley came from Darwin's 1859 publication, Origin of Species by Means of Natural Selection . The appeal this time was to a mechanistic self-ordering process in nature.
Mutations provide random changes and natural selection concentrates the beneficial features.
Of course there are many fatal problems with Darwin's view. However, it is still much used in the design debate. Thus after two centuries, Paley's reasoning still applies and is even stronger than before. In fact, not just one watch has been found, but a whole showcase full, all beautifully constructed and running smoothly. It is further realized that if any of these quantities were changed in the slightest way, the result would be catastrophic.