I believe more than the design of this page, navigation suffers because it isn't clear which page is meant to be the main entrance to the topic. That is the pages often duplicate their efforts (we have links to tsumego, life&death, problems&exercises here for example) and it isn't very clear from the outside what you will get when you follow the link, is it an explanation or a list of problems? If we make this clearer, I believe the list will be shorter too - so maybe design works just fine then.

Joseki, with all the problems still existing on 2nd level pages, is a good example. It is the clear 1st address, when you already know the term and are interested in joseki, it gives access to the main indices and to the joseki tree itself, without overwhelming the reader with tons of links where it isn't clear which one leads to what. Compare this with fuseki, you have an explanation and a link to an index, but on the index you find links to other indices, the Overview of fuseki patterns isn't linked from the main page etc. etc.