The current system is much more fair than the previous one and is similar to what is used by IMDB (The Internet Movie Database).
Check out http://www.imdb.com. It's even more popular than WinCustomize.
Any person can vote on a movie that is in their database. However, only a subset of those votes (registered users) are used to calculate the all time best/worst/etc. movies.
Similarly here, we track the downloads of all skins because 99.9% of skin authors will never be in the top 10 lists on the site. But they are certainly interested in seeing how many people downloaded their skins. And we track the top 20 or so skins/authors on their own seperate page.
But for what is displayed here, we use registered users. This helps avoid intentional/unintentional manipulation of the list. In addition, statistically, the rankings should not fundamentally change.
But as the IMDB example shows, WinCustomize is not the only one who uses a subset of its user base to determine top 10 rankings and they do it for the same reasons we do.