I think there are still things that WAR doesn't capture, especially for catchers, things like ability to handle a pitching staff, giving pitchers confidence in throwing hard breaking balls with runners on base, etc.
WAR is excellent in general, and I like it in many circumstances, but catcher defense may be one area where it doesn't tell the whole story well. Fangraphs themselves readily admit this:
http://www.fangraphs.com/library/defense/catcher-defense/