Many have responded to this old canard, such as Bill Dembski in The Design Revolution and myself in my forthcoming book, Christian Apologetics. "God of the gaps" just presupposes that naturalism can explain everything; if it faces an explanatory problem, it refuses to consider a non-natural explanation involving original, intelligent causation. That is dismissed as "god of the gaps." It is an air-tight strategy that begs the question in favor of naturalism. Yes, some theistic explanations have failed, but not all. Moreover, many naturalistic explanations have and continue to fail.
Rather than go into a full-fledged, futile diatribe with Dr. Groothuis (as Upton Sinclair said "It is difficult to get a man to understand something, when his salary depends upon his not understanding it!"), I would suggest that you read this long and detailed but very informative reply by Prof. Myers (a biologist, I should add) to a fairly typical creationist plea that ID, a.k.a. creationism, should be taken seriously.
The reply contains some important points, such as the fact that weaknesses in evolution do not in fact represent evidence for intelligent design (as Myers says, "[a]rguing that there are weaknesses in evolution--which are typically bad arguments, anyway, but that's another matter--does not mean that Genesis is right"), or the fact that supernatural explanations are subject to the evidentiary tests of the scientific method, and that scientist should not get involved in debates with creationists because a) they are an eminent waste of time and b) they are just attempts by creationists to gain legitimacy through the credibility of their opponents (scientists).
In fact, you should also read How to respond to requests to debate creationists.
Since Groothuis mentions Bill Dembski's The Design Revolution, you might be interested in reading what a couple of scientists think about it:
The design revolution?
A review of Dembski's The Design Revolution