You can probably do a lot by writing your own css file (I'm sure that the JavaDoc documentation mentions how to include your own), you could also write a custom doclet (hint: google for that term) to generate different output.
But keep in mind that any improvements you could make will probably come at the cost that your JavaDoc will not look like all the other JavaDoc out there. Don't underestimate that, it's a major drawback, because people are used to the look and feel of JavaDoc. Just look how minor the changes to the default look were since 1.3 (or even 1.2? can't remember when they did the switch with the frames).