Quote - I've seen a lot of DC animated movies with Wonder Woman, and she is always in this suit. So why not now? Even the tv series version she was in this suit at the end of the pilot...

In several story lines in DC comics when Wonder Woman went into a serious battle, specifically with a God or someone with Godlike powers, she switched to her battle armor and sword, which generally hid her red, white and blue outfit. The way this outfit is made, the skirt and leather armor could very well hide her leotard and regular crimefighting outfit. 

In George Perez' version of Wonder Woman, she first appears in "Man's World" wearing battle armor to fight Ares' threat and it wasn't until later issues she removed it, revealing her classic outfit once she switched to an Amassador from "Paradise Island"/crimefighting role to tone down her warrior look.