Also you could only get so many seasons out of those shows before the cast gets too old. Are You Afraid of the Dark lasted longer because it could survive heavy turnover in the cast.
There's also the fact that kids will watch the same thing over and over, so there was just less incentive to make larger numbers of episodes. I'm not saying that it's not easier to get kids coming back if you have new episodes, but maybe at the time they had smaller budgets than they do now and it was deemed the more viable business model.
And with the animated shows, something like Ren and Stimpy clearly asked more of their animators than some other shows did. If you watch the James Rolfe retrospective on Ninja Turtles he points out alot of ridiculous errors you can spot in that show, some of which I specifically remember noticing as a kid. I also read a nostalgia article about Tiny Toon Adventures a few years ago that pointed out the fact that not all the animation, even in one season, was done by the same people (I think Ninja Turtles did this too) and it resulted in really variable animation quality.