I think it's a problem regarding the overall theme of the arguments. The plaintiffs' side had one long coherent claim -- what the school board did was inherently of a religious nature, and all the evidence shows it. So they essentially told one story. That's the ideal way to argue -- pick one "theory of the case" and stick to it.
The defense has to cover all the same testimony, but negate that overall theme. They have to say: "Yes, X said ..., but that doesn't mean anything. And Y said ..., but what Y was really saying was ... " etc. Rebutting a dozen different items is inevitably going to be more choppy than tying them all together. Especially when they really do tie together so nicely.
But I also think we have a skills mismatch here and ID got outgunned.