Specific examples? Did you even watch Rocko's? Hell did you actually watch like any of the Nickelodeon shows in the 90s other than Spongebob? They were almost all chock full of innuendo and references that went above and beyond their "target" audiences. I know that you're a Spongebob fan so you're used to just being fed what you're supposed to find funny, but that's kinda the point, if you don't get the reference you can't have it spelled out for you, that makes it not fun/funny (cue "That's the joke" MacBaine, or the Joker's Truth "If you have to explain the joke then there is no joke" or Robot Devil "You can't just have your characters announce how they feel! That makes me feel angry!").
Not even close, especially considering it was just barely in the 90s at all. Spongebob is not more mature, they just toned down the outright gross factor to keep it "kid friendly" while regurgitating the same stuff Nickelodeon had been doing for almost a decade in an even more overt manner. The reason Spongebob makes it into a "full theme" is because it took things to an even lower common denominator level, and caters to the people that didn't get all the jokes and references of those other shows (even though they were far from subtle about it most of the time) and then slaps them across the face with it constantly so they'll get it. Kinda like the laugh track on crap like Big Bang Theory, they have to almost outright tell you to laugh, but that just makes it less funny.
Spongebob is by nature a lesser breed. The great tongue-in-cheek comedy of the 90s was done in, and they needed shows that were more direct while also being even less offensive to appeal to an even wider audience. Its good in many ways, but ultimately is let down by dumbing down its greatest strength.