The suboptimality argument against ID is looking more forceful than I originally gave it credit for. On the surface, it does not seem worthy of much serious consideration - merely a theological objection meant to make certain theists feel uncomfortable about God's competence.

But if it is interpreted as an argument against the validity of ID as a legitimate research program, it gains considerably more weight. Here is the problem: Design theories must be predictive. They must explain features of the natural world better than their competitors, suggest fruitful new areas of exploration, and make verifiable predictions.

Is it predictive to simply draw design inferences from isolated biological structures, without explaining why life sometimes appears elegantly designed, sometimes incompetently designed, and sometimes undesigned (i.e., the result of evolutionary processes)?

Well, not so much. I don't mean to disparage the legitimacy of isolated design inferences, but they would gain much more weight if they could be placed in a framework that explains why life does not appear to be uniformly well-designed and (crucially) where we might or might not expect to find design in the future.

This is not a small problem. In fact, I think it is one of the central challenges of ID: not just to create a statistical test for design, but to craft a creation story that incorporates and supercedes the evolutionary one. A story that provides a framework for discovering precisely what was designed, where, and when.

This is not to say, by the way, that evolution does not face the same dilemma of reconciling the existence of both elegance and kludge in nature. It is not really taken seriously by evolutionists, however. Evolution is smarter than you when it produces elegance, and dumber than you when it produces jury-rigged contraptions. No further explanation is required or expected,  because time and natural selection are presumed capable of creating, well, whatever we discover.

This is why I think design theorists are in a better position to explain the disconnect than evolutionists. We take the problem seriously (or we ought to), because ID allows us to distinguish between the mechanisms responsible for elegance and kludge. That is, for ID the question is distinguishing chance from design, for evolution it is getting design from chance. Better to have a problem of sub-optimality than a problem of optimality.

How can design theorists address this problem? First of all, we need to stop accepting suboptimal design as a real but unimportant (to ID) feature of the world. The very thing that makes ID falsifiable is that it makes certain minimal assumptions about the designer - for instance, that he designed in such a way as to be empirically detectable (as opposed to simply mimicking chance). In accordance with what we know about the molecular machines in the cell, I think we must also assume that the designer is not only competent but a great deal more advanced than we are. If ID is to make predictions, it will not do to say that he alternated unpredictably between elegant and inefficient designs.

If instead there is a reason that some biological structures appear elegant and others appear inefficient, it should be discoverable. In order to discover it, however, we need a specific theory of design. Exactly when did design occur? In the first cell and at the cambrian explosion are hypotheses which I have heard, though I think some would see design as more pervasive than that. We need to know. Occam's razor will be helpful here - frontloading and fewer design events should be preferred over more pervasive design, all things being equal.

From the design events, we can infer a trajectory. How did design progress? In an analogous way to technological evolution? Not at all (that is, designed structures appear fully complete and do not improve)? Some combination of the two? And what role does (or doesn't) evolution acting on front-loaded information play?

All of this should help us pin down where sub-optimality arises. For instance, if designed structures appear fully complete and fairly early in the history of life, you would expect most highly-conserved structures to be elegant and efficient. Sub-optimalities should be relatively unconserved and recent in the tree of life - presumably due to the accretions of chance, and in principle distinguishable from design. 

A fruitful theory of design such as this, which explains sub-optimality and successfully predicts where it ought/ought not to appear, would go a long way toward legitimizing ID as a science.