Prime had great CGI for television. And some really good storie and character moments, too. (Look up on Youtube Ratchet bellyaching about humans in season 3, and the entire crew just staring at him).
Overall, it wasn't as good as Beast Wars, though. Too hit and miss. The focus on "collectibles" and Predacons didn't help.
Still, I rewatch it from time to time.
So yeah, imo if we go by era, the 1980's is defined by the Adventures of the Galaxy Rangers. Nothing else even comes close.
The 1990's had a lot of good animation, from Batman to Freekazoid, The Tick, Spiderman, Animaniacs..
But for my money, Disney's Gargoyles stands out because of its writing, subject matter, and general sophistication. That, and you can't beat David Xanatos as a villain/anti villain.
And for 2000's, while you've got amazing shows like Justice League, Batman: Brave and the Bold, Kim Possible, Gravity Falls, Star Wars Rebels...
But imo Avatar: The Last Airbender wins hands down. Even if I personally prefer Gravity Falls to just about anything (And apparently am one of the few who liked Batman: Brave and the Bold, mostly because of the obvious Adam West era influences, but also for the way it gave exposure to Blue Beetle, Guy Gardner, Adam Strange, Desperado.. Not to mention, a hillarious Super Dickery montage.)