a lot of things coincided to produce the 1989-2000 animation boom: reagan-era deregulation and the still-profitability of saturday morning cartoons (which led to batman), cgi still being in its infancy, late boomers/gen x writers (who were influenced by things like rocky and bullwinkle and were generally more willing to push the envelope), etc. a lot of it was basically a happy accident.
also, digimon was bad. it was the poor man's pokemon in more ways than just the title.. and i knew that even as a 10 year old. but for some reason i watched anyway. i guess the characters were cute if bland. granted, the premise was actually pretty good (certainly better thought out than pokemon...) even if it totally failed to live up to its potential.
There's plenty of good animated series still airing new episodes (Adventure Time as Lief said, Regular Show, Gravity Falls, the very controversial one about horses, etc.)
Spongebob was good until about 2004 or 2005 before they replaced all the writers.
yeah but those are very much exceptions to the general trend. the 90s really were pretty remarkable in terms of the sheer volume produced in movies and cartoon shows that were critically well received. whereas something like say, nostalgia over '80s cartoons tends to be just that.