While I did like the cartoon, it really did a number on a lot of the characters. Batman became all about his "bat gadgets", Robin did whatever Batman did, Aquaman was basically the "fish whisperer". Zan & Jayna were comic relief.
The difference is that the other characters had a long history with DC Comics, so that balances out what their appearances on the show was. There were also other media that came after Super Friends......TV Shows, movies, other cartoons. Zan & Jayna only were known by Super Friends. Most people didn't know there was a Super Friends comic book, nor did they read Extreme Justice or Young Justice, so the Twins are remembers as they were on Super Friends.