I have touched on the Intelligent Design bebate before. (No, really? - ed.) Much of the debate is marred with with significant scientific illiteracy, particularly on the scientific definitions of fact vs. theory.
The title of this post refers to the best possible description of the scientific process: the scientific method establishes an evolutionary environment in which theories must compete and advance toward the best possible description of the world. Those familiar with the concept of memetic evolution will recognize the analogy, but I won't go too much into the terminology of that framework. Having multiple theories attempting to explain the same set of facts is, temporalily, a good state of affairs for science. The competition of theories will drive investigation into the unknown areas of the world of facts via experimentation.
Ultimately, however, the competition needs to be resolved. Merely proposing a theory that points out weaknesses in existent theory is not enough. The new theory has to actively set out to prove that it is the superior theory by virtue of being the better fit to the world of facts. If the theory of intelligent design is to be taken seriously, it must proactively seek to describe current known facts and all facts that are discovered over time. In the end, one theory or another has to be the better fit in the world of facts. Like the losing creature in the environment must either adapt or die, the proponents of Intelligent Design (scientifically the clear loser) must either amend their theory or sit down and shut-up.