I've looked at a lot of data I had taken earlier last year from the previous Gamespot site, and compared it to the new data. Here's what I think happened to the user ratings and Average Player Score.
The old site worked fine. If you wanted to give a user rating (rather than a full written user review), you'd just go to the page for the game you played, you'd go to the version of the game you played (PS2, XBOX, whatever), and you'd give a rating. That rating would be added to all the other ratings for that version of that game, and Gamespot spat out an Average Player Score.
When the site was redesigned, for whatever reason, there were no longer separate pages for each version of a game. You could no longer see what the Average Player Score was for any given version - all you could get was the overall Average Player Score across all the versions.
When Edgework and others from Gamespot saw this, they fixed it by separating out the versions. The problem is that the new site still only has one page where you can give a user rating for a game, and that user rating isn't version-specific. So Gamespot uses some kind of algorithm that compares the sales of the various versions of the game, and assumes that you are rating the version that sold best in the given time period. You think the PC version of Batman: Arkham Asylum is bad, so you give it a low rating vs. the PS3 version? Nope. You just rated whichever version of the game sold highest.
Either because the old data was lost, or for some internal policy reasons, Gamespot then applied this algorithm to all of the old user ratings and old Average Player Score. So if, for example, a game came out on Gamecube, Xbox, and Playstation 2, because Gamespot no longer knows which user ratings go with which version, the algorithm automatically assigns most of the ratings to the highest selling version of the game. That's why you can look at any older game and you'll see 90% of the user ratings under one version of another. Go ahead - I challenge anyone to find a multi-platform game where the number of user ratings assigned across the various versions makes any kind of logical sense.
It's frustrating, because the Average Player Scores can't be remotely accurate any more - and regardless of what I've been told by Gamespot, the data indicates that the numbers made sense before the redesign.
I remain of the opinion that I'd rather Gamespot just start the ratings-only user reviews over again from scratch than give us admittedly inaccurate information. It sucks that Gamespot had the largest database of user ratings of any site on the internet, but at least with IGN and Gamefaqs, the user ratings appear to be accurate.