OK, it wasnt ABC that did that, it was the Disney channel. The Disney Channel also went back and edited parts out of hte first two seasons that aired on ABC, and now air only on the Disney Channel. I agree though, the third season that aired only on the Disney Channel(Goliath Chronicals or something like that) was a big let down, The animation quality went way down, not to mention everything else. Also, Xanatos let them back in the Castle on, what was supose to be, the last episode of the series(end of the second season) because they saved the life his son twice. It was hardly out of character at that point.
Also, I though the newest Jonney Quest episodes were pretty good. They even let some cursing and death slip by on that show(this was way before adult swim or even uncut GW at 1am)
No, it was the predecessor channels to UPN that ran the "Disney Afternoon" cartoons, which first aired "Gargoyles" as a more serious kiddie show. The third season "The Goliath Chronicles", with the Stonecutters or whatever they were called, was aired on ABC as part of the Saturday morning line-up. Later, Toon Disney grabbed the show, and as you said before, editted all the good stuff from all the seasons.
It pisses me off, because Noggin has done the same thing to "Daria". They cut out all the swearing, sexual inuendos, and all the adult stuff that made it funny in the first place. It also doesn't help the show is on just before that crappy Canadian middle school show "Degrassi".