In my view the current state of Evolution Theory suffers from a serious problem. Anything that challenges not only the general idea of evolution but many of the specifics is labelled "unscientific". I think the general idea of evolution theory - that people evolved from lower forms of life is likely correct. I also think that teaching a literal intepretation of Genesis is not something to be done in the science class.
But it is not unscientific to look at a complex structure such as the eye and try to see if it is reasonable to think that it evolved or was designed. That's a thought process that students should go through. Teachers of Evolution should be able to defend their position on this subject. In my experience in Evolution classes this thought process was not explored properly at all.
I go further though, becauseI happen to believe that the Neo-Darwinian model of evolution is probably substantially wrong. I've heard some great challenges to it on the basis of experimental findings and mathematics. And these challenges come from what looks to me like a growing group of people who are not pushing religion. I think the fear from a lot of people is that a debate over the particulars of evolution will lead to a religious crusade. So for this reason a lot of the refinement to the theory that I think should have happened has not made it to the classrooms.
I'm troubled by the thinking that I see in evolution classes, where ideas are presented as fact and not seriously proven. In high school and college I challenged recapitulation theory, the molecular clock hypothesis and some of the fossil evidence for human evolution that was presented as factual. Students I think need to be able to tell the difference between facts and theories.
So I think its healthy for evolution to have to defend some of their ideas vs "intelligent design". In my mind that is the one of the basic ideas of the theory of evolution - to explain why some things might look as though they are designed but were not. The book of Genesis vs evolution is the inappropriate context for the science class.
I think its nuts to define "intelligent design" as only a religious subject and something science can never consider. It gives scientists a pass on seriously proving a theory in the classroom that is supposed to explain why intelligent design is not the answer.
Having said that I think we still have to be careful on what the components of inclusion of "intelligent design" in a course curriculum really means. The whole class can't be a debate and the theory of evolution needs to be taught
thoroughly because it is very important to understand. I just think Evolution theory as presented in high school/college introductory classes needs some serious house cleaning. It's got some problems with data integrity and scientific method in it's presentation.