The "similar" list is mostly a mess anyway since hardly anybody know what to add. On the page for The Wonderful 101 I've seen Okami, Viewtiful Joe and Bayonetta listed as "similar" games when they clearly could not be any more different. All they have in common is they were created by Platinum Games (formerly Clover studios) and directed by Hideki Kamiya. I feel that is true of quite a few corners of the wiki that are quick and easy to edit and thus get turned into a mess by drive-by editors.
Franchises are also very confusing. Is Super Paper Mario part of the Mario franchise, Paper Mario franchise, Super Mario franchise and Mario RPG franchise? Why are there no sub-franchises, for example. All of these are part of the Mario franchise but shouldn't that be a given when they are first and foremost (going by Super Paper Mario) part of the Paper Mario franchise?
Wikipedia's template solution is tried and true. Check out the bottom of Wikipedia's Pac-Man entry for instance. It has an over-arching franchise, then divides it by console, with lists. A table template of this sort would work very well to keep things tidy, as (and I keep repeating myself) would franchise portals. Launch-points for major franchises, consoles, etc. There should be a "Mario" portal, with an organized overview of all things Mario. Each subpage would have something like the aforementioned wikipedia grid at the bottom (or top, or...) to navigate. See: http://en.wikipedia.org/wiki/Portal:Mario ... but better, because GB has no real notability or source requirements (which is a VERY good thing), so you could really drill into the Mario universe with a good portal.
Consoles would be similar, but with accessories, games, companies, etc... The thing is, the data is already in place, it just needs some database kung-fu to populate everything automagically. Right now, GB's wiki reminds me of the very early days of Wikipedia, but unlike wikipedia, there isn't a centralized repository for tweaking, only this forum, nor is there a very useful best-practices guide. There are a few stickies on the forum that provide some guidance for new editors, but a lot remains to be fleshed out.