I think the new organization you are proposing is a good idea, and I especially like any suggestion that features downloads more prominently on the front page. You can take it further and also show the most recent reviews too (right now, when reviewing something old, it's pretty easy to go unnoticed). On the other hand it would be hard to implement this feature without showing too much, and turning it into a gigantic list of unsorted information.

One suggestion I have is that you might want to just have links to all big JJ2 sites right on the navigation bar. There aren't really that many active ones besides J2O. One option is to list the big ones in the navigation bar (jazzjackrabbit.net and JDC come to mind) and the smaller ones can go under some "Other" page which lists the rest. I think that's probably better than always having to navigate to a totally different page.