I became a fan of Monk pretty late into the show's run so I did not catch many early episodes, but thanks to the great cable channel Sleuth (which shows many classic dramas) I have the opportunity to see a plethora of great programs, this one included.
The viewer immediately notices the differences between the two (newer vs. older episodes). They did not go for humor every 5 seconds, and Randy Disher was not a complete joke, like he became in later episodes. But the new ones had their own special appeal as the cases were better done, the villains were more evil, and the show was funnier as a whole.
But you have to love the quirks, and how original Adrian Monk was at the time. The broken blinds, littered paper and water on the desk would have irritated me too.