You DID get a S3 of YJ, it's S2 and S4 that we didn't get.
Young Justice is weird, it feels like Greg planned for getting cancelled and only getting one season out, because S1 is pretty self contained with only a few plot hooks for the next season, but didn't have a plan for if he got cancelled after two seasons.
Because it's pretty clear than YJ was supposed to be a 4 season arc.
Best as I can tell, the plan was something like this:
S1: Setting up the team, the twist, Vandal Savage as end of season threat.
S2: Deconstructing the old team making a new one, Robin becoming Nightwing, Tim, Batgirl, Wondergirl, SB and MM's breakup, Beast Boy Origin. Final Boss is... I dunno, Lex?
S3: Arsenal, Blue Beetle, Impulse and Time Travel, some cosmic stuff with Adam Strange and the new gods. Aqualad makes his comeback.
S4: Darkseid, Wally coming back.