I once followed STC to the letter (including the index cards), and the result was the worst script I've ever written. Character depth less than a micron. Everything plot-driven (dialogue, storyline, etc.).

I think the most egregious paint-by-page-numbers advice is to put the theme statement on page 5. If a script is so vacuous that you have to force a character to state the theme early on, then the only direction after page 5 is downhill.