Sure, some stories are more enlightening than others, and there is a point of diminishing returns. But I think the stories are pretty useful; they provide anecdotal evidence for various development anti-patterns. They imbue an appropriate sense of apprehension whenever someone says "Source control is too complicated." or "Then we serialize the object to an XML text field..." or "A testing environment would cost twice as much."
But the point of "WTF?!?" is that the stories include blatant, astonishing incompetence.
I've never seen one end "but it turned out there was a genuinely good reason for what made me think 'WTF?', so I learned something".
They're all, "<nelson>Ha-ha</nelson>, even a slightly competent programmer can feel better than those poor saps!"