I have favorites from many eras.Ghibli's Lupin, Gunbuster, Cowboy Bebop, FLCL, and The Tatami Galaxy, all come from different decades and are masterfully crafted. However, the best are outliers; none of those listed represent the contemporary industry-wide standard of quality. To define an era, one must look at its baseline.
The discussion of old vs. new anime itself is older than "old anime" if Rurouni Kenshin is anything to go by. As I see it, the main difference in each era is the culture. Audiences change, and different things are trendy at different times, especially with regards to character designs and plot elements. As derivative as modern anime can be, following the leader is nothing new. Even Trigun, one of my favorites, is unmistakably 90s. Good anime and bad anime are distinguished not by degree of conformity but by solid direction and intelligent writing. When I watch mediocre old anime, it appears the lack of these qualities can be traced back to incompetence, whereas the worst of modern anime often seem to be bad on purpose, as though it was cynically decided that the audience is guaranteed to show up regardless. That's the only major difference I can see: anime is more of a business than before. Still, it always was one, and my main point is that era doesn't matter if you avoid the fodder.