After 2 successful seasons, WB decided to risk messing with the concept of Justice League by expanding the scope of the series and its cast, thus the title change to Justice League Unlimited in 2004.
While the League's roster expanded to seemingly infinite proportions, using a number of characters that hadn't been active in the comics in quite some time, the producers opted for longer story arcs as well. Chief among those was the introduction of the Secret Society of Super Villains, which was also revived in the comics around the same time. The Society's TV incarnation used an upgraded version of the Legion of Doom's Hall of Doom (the Darth Vader helmet-shaped mobile HQ from Challenge of the Super Friends) as their base, and like the League, had a pretty deep roster to work with.
However, one of the better episodes of the series was the season 1 opus, "Kid Stuff", in which Superman, Green Lantern, Batman, & Wonder Woman are transformed into kids to thwart Mordred's plot to take over the world by banishing adults, including his own mother, Morgaine LeFey, whose nemesis, Etrigan, the Demon, also appears. Most notable about this episode is that the juvenile Amazon is voiced by actress Dakota Fanning.
Here's a sample of "Kid Stuff":
By this point in the series, there were hints of a romance between Wonder Woman & Batman, which started in "Starcrossed: The Movie". Unfortunately, it didn't last long. Flirting certainly seems to be out of character for an Amazon, doesn't it, though?