I doubt this will get anything done but it can't hurt!
Would it be at all possible to get a navigation system better than "gigantic list of links"? The leaning tower of links may have worked in 2000, but it has not aged well as you've added 540 new games and 255 new TCG sets and 4 new anime sagas to it. It also works very poorly on game pages with large numbers of subsections.
Some suggestions to that end:
1)Either blatently sort games by gen(as in, have each gen be its own "section" like we have the anime/video games/TCG/etc. sections now) OR seperate main games from side games. I shouldn't have to squint to find, say, Ruby and Sapphire squished between various Ranger/mystery dungeon/Gamecube games. If you sort by side games, try to clump similar side games together(ie. all the Mystery Dungeons would be together, as would all the Rangers, all the Gamecube games, etc.).
2)Move the movies/Pikachu shorts into the main Anime section. Have a "movies" link, and have that lead to a list of the movies & shorts(ala the lists of episodes in each saga). Or at least move the movies/Pikachu Shorts sections right below the anime section, because it's pretty silly to order things "anime" "video games" "(anime) movies" "Pika shorts".
3)You know the lists of links in each video game page? For the games with more than, say, ten pages, split their listings up into sections. Example: HGSS is currently a bloody mess that makes it difficult to find anything not at the very top or bottom of the list. Putting graphics with "Pokemon", "Events", etc. to obviously split up sections would make it easier to navigate. Looking at it now, you already have things kind of split into subsections, but making those subsections more obvious would do wonders to make video game pages easier to navigate. And looking at the Ruby/Sapphire page, you actually did this once, and it really did make the sections easier to navigate.
I know this would take precious time away from Project Mysterious Myster...I mean, Valhalla, and there's so much news now that you legitimately have less time to work on the site itself, but fixing the site's layout NOW will be easier than having to do it later, when you have more info to move around and more pages to update. And the layout has to be updated eventually, right? Right? Right?