1. This is the big league's gentlemen.
As mentioned, this doesn't necessarily make it better. The "big" storylines are great, but when you save the universe every week, every threat just has to get bigger than the one that preceded it. I felt this way with Morrison's JLA run. It's not a bad thing to have the big stories by any means, but it's also not bad to have smaller stories that lead to the big events.
I would say that this is one of the things that differentiates the Avengers from YJ, and I can definitely see this as a positive depending on your tastes.
2. Better guest stars
Will have to see at the conclusion of Season 2. In Season 1, YJ definitely felt like it had the more expansive universe. Now with the 5 year jump and the introduction of a whole new cast, this is again arguable.
3. Better Characterization
This I disagree with. Avengers does do the huge storylines, but in doing so the personal smaller stories are somewhat glossed over. Young Justice spends way more time in characterization and through Season 1, you feel like you know each member of the team very well. It's the only way they could have done the story where the Light attempts to turn 3 members of the team.
This is not to say that the characterization in Avengers is off, because it isn't. I think they nail the characters as well, but YJ focuses on them. Avengers is more about the big picture and the huge storyline.
4. Hulk is actually on the team.
K. But you know that doesn't make it a better show.
5. Better Villains
Did you conveniently leave out Lex Luthor (star of comics and like every SUperman film), Ra's al Ghul (star of comics and film), Bane (star of comics and soon to be in one of the biggest films of the year), and Vandal Savage?
C'mon now. More people know Lex Luthor and Ra's and Bane now than most of the Avengers' villains you've listed.