The problem with Intelligent Design is that it's not a theory. It's an argument against a theory. Its primary purpose is to debunk evolution, and even then, only does it by misstating evolution or by pretending that a few gaps in a theory completely undermine it. In essence, it's not a theory; it's a smear job.
And this is complete garbage. Science is nothing if not self-doubting. That's the essence of science. Far from the monolithic conspiracy many anti-intellectuals suppose it to be, science is curiosity and doubt formalized into a coded study. So there is no reason that doubts and questions and gaps in evolution need to be formed into a competing theory. Imagine Einstein using his ideas on Relativity and whatnot as a refutation of Newton, rather than an addendum. If evolution can't incorporate these questions and gaps, then it isn't science. But it doesn't gloss over those differences. In many cases, it answers them fully. And in other cases, it is still in development. Only in the minds of creationists do these "flaws" warrant the complete usurpation of evolution that they imagine.
This is due to differences in their intellectual processes, which require fully conceived answers to all questions. This is why, at its most basic, religion must be in opposition to science. Science is made of questions looking for answers. Religion is made of answers looking for questions; and they're not allowed to ask the questions that don't already fit the answer. That is why they consider gaps in evolutionary theory as fatal; because they fail to understand the basic premise of science. Rather than an ever-growing body of knowledge, they see it as an upstart religion that just hasn't gotten its act together yet. As if we had tried to present a solid theory of life, but screwed up on the details and are just making stuff up as we go along. To them, each scientific revision is a laughable error. Each gap a ridiculous oversight. Just as God created the universe in six days, they expect scientific dogma to be bestowed upon us from above in its entirety. It is ironic that they fail to understand the evolving nature of science itself. For them, not only did man not evolve, but his theories didn't either. To them, science is just yet another attempt to destroy their god.
But in no case should these questions and inconsistencies be considered a separate theory. And again, their mistake is that they see science as another religion. Many religious people consider minor differences over unknowable historical events and insignificant rituals as irreconcilable differences; requiring different factions, each competing with (and often hating) the others. With Intelligent Design, they continue with these same standards of intolerance. But scientific inquiry has no such demands. Legitimate questions, disagreements, and revisions are all part of the scientific method. These aren't competing powers attempting to woe the masses to their side with pre-conceived answers; these are people working together to find the answers. While scientists may have their personal feuds, at the end of the day, they're all on the same team. A Christian who perseveres with their beliefs against overwhelming opposition is considered a martyr. A scientist who does the same is just a bad scientist.
Worst of all, the only reason why ID is even considered to be a theory is because it really is intended to be the scientific replacement of creationism. Creationism is a theory. It's non-scientific and evangelizing in nature, so it can't be taught in school, but it is a theory. But ID is not a theory. Separate from creationism, it exists only in relation to its ability to debunk evolution. And if it isn't just a repackaged creationism, it can't be taught as a theory. Because it's not one. Its intent is to deceive, providing intellectual cover for those not capable or willing to understand evolution. It thrives on ignorance and can only work in the absence of scientific knowledge. It's intent isn't to educate, but to confuse. That is why the fundamentalists like it, and why it can't be taught in school. These people aren't trying to make religion into a science; they're trying to make science into yet another religion. And all due to ignorance on the very subject that they need to understand most: Science.
Post Script: This shouldn't be necessary, but I just wanted to say that this post only applies to fundamentalist Christian-types who believe in Creationism and/or Intelligent Design. But to my knowledge, these Christians are a minority, and most Christians believe in evolution. Even the Pope supports evolution (or at least the last one did, I'm assuming the new guy does too). So you should always take that into consideration on all this stuff. Extremists are always loudest because there are so few of them. So you should always strive to marginalize the extremists, and not lump them into the majority. But then again, perhaps fewer Christians would believe in evolution had the "other alternatives" been taught in school; which is exactly what the extremists are working at.