I feel like cartoons of what people call "the 90s" (aka like 1985-2004) were generally pretty great, yeah, but there was a lot of crap on that people forget about I'm sure. We're kind of comparing the highlight reel of that era to the entirety of what we've been looking at since then. And I wonder honestly how many people who praise that era of cartoons have actually gone back and watched them recently? In a critical way, to see how they hold up. I've been doing that recently.
Code Lyoko's kinda slow but still good. Sailor Moon takes for flippin ever to get going. Hey Arnold and Teen Titians are fantastic. The Proud Family, Kim Possible, and Jake Long were wonderful. The Jimmy Neutron movie was great, but the animated series was hit or miss. Billy and Mandy, Doug, Pepper Ann, Recess, Dexter's Lab, PPG, and Ed, Edd n Eddy are fine but lack a decent amount of plot to keep people invested. A lot of them were like that; made for being self-contained episodes that eventually just got repetitive.
Seriously, I loved that era of cartoons. I will absolutely go watch Boomerang for eight hours and enjoy it (wait, is that still around?). And there's no doubt there was a bit of a cartoon crash around 2006-ish. Like about when regular network TV stopped really having Saturday Morning Cartoon programming. There were a few gems in the in-between times, like the first two Total Drama series, Avatar, Danny Phantom, you know. But I think great cartoons are making a comeback now! Legend of Korra, Adventure Time, Gravity Falls, Steven Universe! Over The Garden Wall! LoliRock is looking promising, as is Star VS The Forces of Evil.
Thing is, they're story shows! The ones I'm becoming invested in. And when I look back into my Cartoon Golden Era lists, there's a very similar amount of story shows that I enjoyed! So maybe it's not that there're less great cartoons now. Maybe it's that we enjoy a more select group of them.