I’m not a biologist but as I understand it, biologists no longer regard natural selection as the only mechanism for the change between body types. I suppose that’s so for the reasons you’re giving: natural selection by itself doesn’t explain the rise of phyla, for example.

If you look at the relevant section of the Wikipedia article, you can see several naturalistic explanations of the Cambrian Explosion. As limited or speculative as some of them might be, any of them is necessarily superior to supernatural Intelligent Design (because of methodological naturalism). Creationism has only emotional value but no explanatory force. Saying that God created life by a miracle doesn’t increase our understanding, but would only stultify us if Creationism were universally believed, making us doubt our cognitive faculties and turning us into mental (and eventually physical) slaves. The consequent theocracy would be like a globalized North Korea, as Christopher Hitchens used to say.

I’m reading a couple of novels based on Lovecraft’s At the Mountains of Madness, about the ancient aliens scenario. These books posit that amoral aliens created all life on our planet for sinister reasons. The aliens mean to enslave or consume us — but at least they’re only mortal, albeit superhuman creatures. Theism makes nonsense of all human intellectual progress.

Of course, such unpleasant consequences don’t make Intelligent Design false, but the latter’s explanatory emptiness means there are only the moral and aesthetic criteria left to apply to such a pseudo-explanation. On those grounds alone I’d be inclined to discount Genesis, say, as an “explanation” of how organisms came to be.