> Arbitrarily adding fonts, colors, and background images take a perfectly usable layout and make it look like something straight out of 2002.

For sure. I've seen a lot of these "improve bootstrap" articles that advocate adding fonts, colors, etc. But, at the end of the day, the webpage is still obviously twitter bootstrap with a few tweaks (almost always for the worse. I'm not a designer, but "oversized header + buttons for links + 2 or 3 columns below the header" (and often with something functionally equivalent to a menu bar at the top) is so clearly bootstrap that I don't understand making any effort to hide it.