Batman: TAS is a much better show than Justice League. Actually, Batman Beyond is a better show than Justice League, but it also aired smack in the middle of both decades and it's hard to really place it on a list. I can't call Disney shell outs like Tale Spin/Chip and Dale as good a Tiny Toons either. IMO they don't even really feel like a 90s toon.
If you're wondering the shows I cut from teh 90s list are: Eek The Cat, Darkwing Duck, X-Men, Pepper Ann, and Bobby's World.
From the 00s I cut Rocket Power, Teenage Mutant Ninja Turtles, Camp Lazlo, Sponge Bob, and Megas XLR.
Yes the 90s had a lot more original content with daily new episodes, and fast season turnovers, but those days are over. But I'd say the big things are the emergence of Pokemon and the anime wave at the end of the 90s early 00s which pretty much started to fill in more and more slots.
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Chrono1219
The beautiful genius who graduated from Harvard as a child and has an IQ of 1.3^googolplex.