Intelligent design says some features of the natural world are best explained by an intelligent cause because they are well-ordered and complex.
I would like to offer a question to the intelligent design side: Why can some species of tortoise not right themselves when they fall onto their backs? Certainly this is a serious design flaw that a truly intelligent creator would have spotted in design or at least issued a recall.
Why would evolution have not made a perfect creature? Because evolution does not work to perfection, only to "good enough". A creature only needs to be good enough to be the best within its own ecological niche. All of the wonderfully tuned species are the good enough results of some highly competitive niches. One might as well ask why elephants aren't stronger or eagles don't have better vision. The loss of a few tortoises from falling onto their backs is a relatively minor flaw, one that does not threaten their niche possession. It may have been a greater problem in the past, and I think (not really wanting to do the research right now) that it was made less of a problem by lowering the tortoise's center of mass or expanding its base, both of which decrease the likelihood of falling over in the first place.
So, in my mind, one of the key questions that intelligent design needs to answer is not why the natural environment is so well-ordered, but why it is not perfect.
For a much more detailed view on evolution and genetics, I recommend that you check out Gene Expression.