Absolutely wonderful--I couldn't agree more! Rules should compliment the game, and forcing rules to do things they are poorly suited for detracts from the game. This is why d20 both sparks my admiration and annoys the hell out of me.
d20 is very flexible, and with a little work you can often adapt it to a variety of themes. It is very modular, allowing you to swap out some rules while keeping others. Once you learn the basics it is easy and intuitive to change. But aside from the heroic fantasy described in the article, it doesn't do any of them particularly well. Unfortunately, it is so ubiquitous that many people do not even consider alternatives. And even more unfortunately, games that used their own, perfectly suited mechanics often succumb to the temptation and put out new editions in d20, even when their original rules were far superior.
My absolute favorite game so far is the Legend of the Five Rings RPG, which is a samurai fantasy game. It uses a system known as Roll & Keep, and the melding of game, setting, and mechanics is absolutely flawless. Understanding the rules means you understand the setting better, and vice versa. It also just "feels" like you are playing a samurai character--the dice are very dramatic, and on any roll the sky is ultimately the limit, but there aren't really any botches or critical failures. It simulates playing a samurai who has trained rigorously for his or her entire life, and so isn't prone to undignified mistakes. Rather, as you progress the bar for achievement simply gets higher and higher--in the beginning, you are simply trying to hit your opponents. In the middle, you can generally hit your opponents without a problem but the challenge is now to hit them and kill them in one blow. At the height of your character, you can hit without a thought and generally succeed in killing without effort, but the challenge is to kill honorably decapitate your opponent, leaving just a thin bit of flesh to keep his head from rolling around and insulting his family. Or, by the end of the game your character is so enlightened that he realizes killing others really kills him, and so the challenge is defeating opponents without striking a single blow, by using his influence and reputation. The rules perfectly compliment these sorts of ideas, the idea of chasing unattainable perfection, and without those rules the game would be greatly diminished, because the actions that make sense in the setting also make sense under the rule system.