This is not really an answer to your post but a notion that popped up while reading it. Since you seem thoughtful, maybe you'd be willing to take a crack at responding to it.
What if ID were true but our glorious selves were not the "goal" but a trivial side effect of the designer wanting to breed more and better bacteria?
That is an interesting point. I am curious though by what you mean by "better" bacteria? Did you mean "better" as in bacteria that would be resistant to anti-biotics or to immune systems? If so... then there is a problem because there is only one way bacteria becomes more resistant; genetic selection through a series of generations. This is also known as "survival of the fittest", genetic adaptations to environment changes or... evolution.
And so... the Intelligent Designer would be using evolution for creating "better" bacteria. The problem is it would be proof that evolution does exist. I was under the impression that evolution and ID were mutually exclusive (am I wrong?).