I've read the entire run of the 1999 Young Justice. I liked it for the most part. Sometimes it just got too silly, even for what it was. I like Fite & Maad, though, and Cissie was great (I enjoyed her friendship with Bart, liked her issues with her mom, and thought her story where she left the team was good, if ultimately unsatisfying for not being revisited). Didn't like what they did with Traya (prefer pre-crisis more "normal" Traya and I didn't think she should be hanging out with teenagers).
But my biggest issue was probably Secret. I'd say her arc is probably the closest the comic has to an over-reaching arc. And I liked Secret fine at first. But the more I read of her, the less I liked her. She's the weakest link to me. Or rather, the character I was least interested in.