One criticism levelled at intelligent design is that often the arguments amount to god-of-the-gaps where the designer is placed in a gap of our knowledge. An example would be that since we don't know how the bacterial flagellum developed, to invoke a designer would just be taking a gap in our knowledge and saying "God did it".
The response I often hear to this is that calling it a god-of-the-gaps argument is misleading, but that design is a positive inference based on what we know about designers. What we sceptics see as an ad hoc invocation of the supernatural is really taking the best explanation in terms of what we know.
The problem is, however, that the best explanation doesn't mean good explanation. Take the bacterial flagellum, if the evolutionary sequence leading to a bacterial flagellum could be discovered then what makes a designer any worse or better of an explanation? It's just the best explanation in the absence of a good explanation.
But to highlight the absurdity of this design inference, take the idea of lightning. Thousands of years ago people didn't know why there was lightning and invented gods to explain it. The problem with those arguments, however, is that there was no grounds for supposing agency was behind it. But now that people have come to be able to generate lightning, does that mean that now agency is a better explanation? And of course since we don't see people nor aliens in the sky making the electricity, one would assume it's of supernatural causation.
Sometimes the "best explanation" is indistinguishable from having explanation at all...