Anything that fails to communicate effectively is bad design. You should not confuse illegibility with poor communication. Legibility and illegibilty are very ambiguous and biased terms. Not only are these great designers, they worked at magazines containing great writing. Their editors recognized the value of good design, and a healthy balance was struck between editorial and design.
Emigre stands out.
Unfortunately we've never been considered part of zine culture. Even though Emigre, in terms of its content, can easily be considered a fan zine, due to our design savvy we don't belong. A well-designed independent fan zine is an oxymoron. I can offer no special insights into this. I see good magazines coming from many places.