I think the main issue is like, okay compare this to Justice League Unlimited. You remember those one-off episodes, the ones generally aren't really related to the main plot and tended to be these self-contained stories focusing on specific characters? Like sure they weren't relevant to the wider myth arc, but they were well-liked for offering breaks to the main stories and expanding on the setting by giving these characters focus in the limelight. What helped is the brevity, most of them were only 1 episode long.
Young Justice though takes those stories and turns them into whole-ass arcs. Like the episode where Wonder Woman, and Hawk & Dove team up to fight the armor of Ares in the middle of a warzone, Booster Gold trying to stop a scientist from becoming a black hole, or Green Arrow helping out Canary to get Wildcat out of a superhuman fight club.
Imagine if those stories all took 4 episodes to finish. Again they weren't single-episode stories wrapped up in a neat little bow, possibly to be referenced later or not (like the Ares Armor was relevant to the Suicide Squad episode), but each of those conflicts individually required multiple episodes to tell.
I would say thats the main issue with Young Justice, its too overwrought. Like how Beast Boy's trauma and therapy took up the entire season, which meant most of the time was him not making any sort of progress or doing anything for the majority of the season until near the end.