Andy, while I agree with you on TMNT, that's not entirely indicative of all 80s/90s animation. Look at anything that was on the Disney Afternoon, like Ducktales or Tailspin. I recently sat down at watched Darkwing Duck with my 13 year old brother (I have the entire series on DVD); he'd never seen it before, but he immediately remarked on the fluidity of the animation in comparison to what he's grown up with.
Also, even putting my obvious comic-book-nerd-bias aside, nothing really holds a candle to Batman: The Animated Series, and by extension, Superman: The Animated Series.
A lot of old stuff doesn't hold up, but a lot of it still does. There was just as much good and bad as there is now.