All baseball stats have some sort of measure that can be skewed. RBI's are a function of runners on base and opportunities. HR's can be a function of the park you play in. Fielding % is based on the whims of a score keeper. There are issues with the way WAR is calculated (especially since there isn't only one calculation for WAR).
There is no one true stat that determines a player's value. You need to look at everything.
Now that Topps puts WAR on the back of baseball cards, maybe it shouldn't be treated like a bogeyman anymore. It's just another stat that you can choose to value or disregard.