I think people are putting far too much stock in the fact that Merriman had 10 sacks to Ware's eight. (If Ware had 10 and Merriman eight, would people still think Merriman had a better season?) If you go back and look at each sack for Ware and Merriman, Ware had far more sacks of his own doing, while Merriman had far more coverage/cleanup sacks.
I went back and looked at some video of both players, and Merriman seemed to benefit from his teammates' pass rush on quite a few of his sacks. The quarterback would feel pressure in the pocket and try to scramble out. And Merriman, who was unable to get around his blocker but got fairly close to the quarterback, would grab him or run him down for a sack. In Ware's case, I saw a number of plays when he also pushed his blocker close to the quarterback, just as Merriman did, but nobody else was even close. So the quarterback could just slide in the pocket and throw the ball.
From what I saw on video, and from the stats each player put up against the run (Ware had twice as many tackles for loss and more tackles for no gain), I'm convinced that Ware actually created more big plays and had a better season. But because Merriman had two more sacks, the perception remains that he had the better season.