There are still a lot of teams running their own variety of the WCO; successful teams at that: Niners, Packers, Seahawks to name a few.
The Seahawks drafted Wilson for that reason; as he ran the offense at N.C.St. (and a mix of WCO/Pro system at Wisconsin.)
Then you have the Dolphins, the Eagles, the Titans, the Raiders, the Vikings and the Cardinals that I know of.
Jay Gruden, the Bengals OC, has root in the WCO under his brother Jon; he was with Shanahan for a little while too.
The Browns have been running the WCO, but will probably make the change this year while the Cowboys might opt to the exact opposite.
Andy Reid is certainly going to bring it to his new job; even the Jets and the Bills are said to be getting ready to make the change to the WCO this upcoming year.
Oh, and the Colts made the change to the WCO last year and drafted Luck (who runs it at Stanford.)
Yeah, it's an outdated offense alright!