The modules page is a typical example of a long list that gets hard to manage pretty quick. The categorization is not ideal, with big modules providing their own category and a quickly growing 'misc' section.
The usability tests have shown that after installation, modules do not provide clear starting points to where you can find their configuration pages. Same goes for the new permissions a module might expose. No clear indication that there are new permissions and no clear pointers to where to find them.