Notwithstanding D'Souza's routinely shrill, frequently mocking tone, he does manage to score rhetorical points for his team here and there, but only mostly because Dennett's rebuttal isn't as sharp as it should been.
For example, in this segment (starting at 8:08), D'Souza's argues that modern "Big Bang" theory lends support to the idea that God exists:
Everything that has a beginning has a cause. The universe has a beginning. [Therefore, the] universe has a cause. That cause I call "God."
Now, this argument is really hackneyed. But it is intuitively appealing to "swing voters," and any philosopher with Dennett's skill should have a refutation handy -- something along the lines of:
But talk about "causes" doesn't make any sense outside the framework of time. And on the very theory Dinesh appeals to, time did not exist until the universe began. Therefore, the universe could not have been "caused" in any relevant sense. A fortiori, God could not have caused the universe.
More could be said, of course -- but Dennett didn't even say that much (his rebuttal starts here at 3:30), allowing D'Souza's intuitively appealing argument to go entirely unchallenged. This sort of thing happened way too often.
Don't get me wrong. D'Souza's arguments were generally embarrassingly weak on substance. But you'd need to know something about the substance to know just how weak, and he seemed substantially more focussed than Dennett when it came to rebuttal.