The first two questions that come to my mind along these lines are, why would any intelligence direct, tamper with or otherwise influence the course of life on this insignificant third rock from an ordinary star, and if it's so intelligent, why didn't it do a better job of it?
Well, your question assumes that there is something inherently wrong with the universe, or planet, or organism, or what have you. Its also an assumption that we are ordinary and insignificant. I would agree that the universe certainly appears at times to be something arbitrary. But I have nothing else to compare it to. If this universe is imperfect, who among us knows of another universe that is? Instead of challenging the Intelligence on just how intelligent it is, perhaps it is we that are not intelligent enough to comprehend the sheer genius of it.
At the same time, its a bit of a dichotomy for a proponent of ID, and this is how. Proponents of ID use irreducible complexity as a way to measure the alleged intelligence factor. In other words, they are saying, "look, its clearly designed. These things don't just happen." At the same time, if we are unable to discern what is capricious and what is intended, then how can the ID argument stand as being something obvious?
So is it obvious or are we oblivious?
I think even the most staunch naturalist could admit that some things really do appear designed by intent. And even the most staunch proponent of ID could admit that some things appear random. Perhaps its a little of both. Maybe in some ways both groups are correct in some inferences and incorrect in others.
Edited by nemesis_juggernaut, : edit to add
"The weapons of our warfare are not carnal but mighty in God for pulling down strongholds, casting down arguments and every high thing that exalts itself against the knowledge of God." -2
nd Corinthians 10:4-5