It is interesting to look back at the last 15 years and wonder how often the year end #1 was the best player in the World:
1998 Davenport. No, Hingis was the best player in the World.
1999 Hingis. No, Davenport or Serena was the best player in the World.
2000 Hingis. Definitely not. Venus was the best player in the World and Davenport was 2nd best.
2001 Davenport. Another huge no. Venus was the best player in the World and Capriati was 2nd best.
2002 Serena. Yes
2003 Henin. No, Serena was the best player in the World.
2004 Davenport. No Henin or Sharapova was the best player in the World.
2005 Davenport. No Clijsters was the best player in the World.
2006 Henin. Yes I guess.
2007 Henin. Yes
2008 Jankovic. No, Serena or Venus was the best player in the World.
2009 Serena. Yes, but Safina was #1 most of the yea and was never the best..
2010 Wozniacki. No, Serena was the best player in the World, and Clijsters 2nd best.
2011 Wozniacki. No, Kvitova was the best player in the World (well really Serena was the best, but of course there is no way in hell she should have been ranked #1, but her tennis that summer minus the U.S Open final was the best all year by any women, Kvitova had by far the best year, was the best mainly active player in the World that year, and also should have been ranked #1 by a landslide at years end too).
2012. Azarenka. Again no, Serena is the best player in the World.
So only 4 times in the last 15 years has the best player in the World been year end number 1, twice Serena, and twice Henin. Granted that is not all the ranking systems fault, but it does add some perspective.