I think along with Superman and Batman, John Stewart and Hawkgirl's story arcs are also a lot better. Here, the writers probably benefited from not being tied down to any long-established expectations for these characters. The writers did their thing, and throughout the most part, it works pretty well. After these four, it's a big dropoff to fifth, who's either Flash or WW. I'd say WW is fifth mostly because Flash is mostly there for comic relief, and for scheduling reasons, they completely wrote off Flash for the first season of JLU (I know the DVD boxed sets say there's two seasons, but us fans during the CN run know there were three ). I'd rank Martian Manhunter's as last because even though he didn't have any particularly terrible episodes like I think WW did, his character was probably the blandest, they wrote him off for a large chunk of the last season, and most of his time on JLU he was confined to the Watchtower like the JL's air traffic controller and guidance counselor. I think too much of his character arc revolved around having nervous breakdowns, by the time he left the team as a full-timer, it just seemed fitting.
Outside the main seven, I'd say some of the other characters in JLU were probably written better, too, including Green Arrow, Black Canary, the Question, and Huntress. In limited appearances, I'd say I enjoyed episodes with Vixen and Carter Hall more than I enjoyed any of the JLU WW episodes. Even Supergirl's arc might've been better, though I didn't like the way they wrote her off the show.