The goal of this site is to provide a place for people to discuss the games and, more importantly, a small slice of internet for developers to post news/updates to their projects. For larger projects, this means giving them a board for them to post news and all their users to post their thoughts/opinions on the games. The onus is on the developers to maintain and organize their boards, which means making their projects clearly accessible from their boards.
That being said, there are other reasons I would maintain the current organization:
*Many of the games here aren't downloadable, but links to other sites.
*This general thread would have to be constantly updated by a curator (i.e. me) to make sure all the links are still correct, especially if any upload website is used.
*We already have a general thread about a game list that includes many of the games on here.
I can understand that it might be a bit overwhelming at first, but I feel the organization of the site is satisfactory and reasonably laid out. Most forums have much more complicated layouts and their users deal just fine.