In the case of Spongebob, the writers that everyone hated left and the original creator came back as executive producer. The show has steadily improved since the release of Sponge out of Water.
TTG, to be honest, I have complicated feelings about. I indeed like it, but feel it has that Family Guy factor. Not only because the characters are Peter Griffin-ish, but it has that level of high success ratings security that the writers can pass off idiotic episodes and no one seems to care. I feel the show can be good when it wants to, but would rather coast because it's that popular and doesn't need to impress its audience. Certainly not as much as any of the other CN originals, some being much more fan friendly. I can't stress enough that out of the chibi-sized parody versions of super heroes, Marvel Super Hero Squad was far superior. It knew its audience was kids of geek parents and managed to walk a fine line of kid friendly and having something for the adult fans. TTG is just... odd in that aspect. It's meant for kids, but it gets very disturbing and adult. It has a higher kid's fanbase than an adult one. Otherwise it probably wouldn't be on the schedule as much.
Of course, so wasn't Johnny Test which no one liked (at least past the admittedly watchable first season), but that's because it was really cheap to acquire, as it was cheap to make and got a Canadian Tax Credit. There's actually a line of JT little collector's figures. They went on clearance almost immediately. And at TRU to boot.
When it comes to it, the main gripe I have with TTG is that they're just lazy. It's easier to have them all act like idiots than to have them do something special. That's been the biggest problem this current season. Lots of episodes where they get fascinated by something stupid and the God or King of that something stupid shows up to praise or antagonize them. While episodes like "Fourth Wall" and "Two Parter" actually make the most of the series concepts, but are in short supply. The Rainy Day fun one was especially moronic. I find episodes like that deserve more scorn than ones made to troll the fanbase.