Glynn sent me this article from the Sport Economist on different point structures in different sports, with a focus on Hushovd's green jersey victory over Mark Cavendish. I admit I was disappointed to see Cav lose the green jersey, though I was biased by the fact that Cav was my pre-race prediction. Still, if one equates the yellow jersey with the best overall rider, the polka dots with the best climber, and green with the best sprinter, it's hard to come to the conclusion that Cavendish wasn't convincingly the best sprinter in the Tour -- six stage victories was a dominating performance.
Of course, this year's point total was messed up, as it sometimes is, by the role of relegation. Perhaps it's not the point structure for the Tour that was incorrect, but rather the penalty structure that allows Cavendish to lose all of his points for a stage for a non-flagrant infraction.
I actually think that its the polka dot jersey that has more issues than the green jersey. It's heavily biased towards crazy breakaways. If you happen to make it in the break on a heavy mountain stage, you can pretty much sew up the competition. Great climbers who are also GC contenders have a heavy disincentive to compete for the King of the Mountain title, though it does establish a good secondary contest for climbers who have no GC chances.