Saturday morning cartoons are all but dead thanks to the cable channels and the Internet. Although the 90s also saw a major switch to after-school cartoon programming, as well as a large push towards prime-time cartoons (Batman:TAS and Tiny Toons both started out as prime-time shows! and of course all of Fox's current animation runs during prime-time slots).
Meanwhile, cartooning used to be a much more intricate art form but thanks to digital cartoon production technology it's become much more of an assembly-line process (see South Park, pretty much everything produced by Cartoon Network, etc.) and so since cartoons can be produced quickly and cheaply with very little effort, and written by just about anyone (usually people who have very little understanding of what makes cartoons work), the decline of mainstream animation was basically inevitable.
(God damnit, I sound like a Cartoon Brew writer now.)
I think it's related to time and money investment, if it's going to cost a lot and take a while to animate a cartoon, you're less likely to fuck all that up by using shitty writing.