My main issue with JLU was that it focused on too many characters for me to count or care for.
Now, bear in mind I am first and foremost, always a Marvelite. Marvel has my undying loyalty in most respects (and honestly enough, their recent animated output has been very strong), but I really liked BTAS and all the DCAU shows up until JLU. Something about their shows was just so much more sophisticated and, well, better produced.
The problem is that -from MY perspective- JLU seemed more like fanservice with what I call 'gratuitous fanboy porn' with all these obscure characters showing up. For someone who had -and still has- no idea who Stargirl or Booster Gold are, it's really frustrating. Ultimately, I found both seasons of JLU to be extremely difficult to get into and I just gave up. For me, Justice League ended with 'Starcrossed'.
... Well okay, I do think 'Epilogue' was pretty decent.