If you look at the script you will notice one thing to begin with: perfect cinematography.
Despite the fact, that Timmy is handicapped and therefor temporarily rose to be a hit character, the episode just reflects the talent that Matt Stone and Trey Parker have in their profession.
Although moral is an issue that South Park really looks at with a critical eye, "Timmy 2000" proves to be not just entertaining but also "point proving": Laughing at something odd doesn't mean that people don't care about it! Timmy may be handicapped and amusing, but at the same point the creators prove that he has heart and moral, but furthermore, character! These (if only little) shifts of classical story telling make a very enjoyable episode that will definitely be one of "South Park"'s best! And it also doesn't surprise me at all that the character "Timmy" became a cult from this point on!