Homology: Common Descent or Common Design?

You will often hear creationists criticize homology as being evidence for evolution, because, according to them, it could be evidence of a common designer (eyeroll). Well here's some of my objections to that, and it doesn't so much focus on the similarities that life shares, but the differences that are only explainable via evolution:

* As Michael Shermer pointed out in a debate against Kent Hovind, the fish moves his tail side to side while the whale moves his tale up and down (and when the whale does this he uses the same muscles terrestrial Mammals do when they run). No common design there, but common descent explains this very well.

* Analogous genes. Over half of our genes perform the exact same function as the banana's. So why are they different? Well, if they evolved independently after we split from our common ancestor, the problem is solved.

* Why did God create everything in a nested hierarchy pattern (what we would expect from evolution)?