I think the reason Avatar: TLA didn't make it on here is because the staff at Entertainment just may not care for it that much. I remember reading an article on why The Last Airbender became such a massive disaster in the magazine last year, and one reason listed was that, and Iquote from the magazine, which I have with me
"Sorry, I know it's revered by fans, but the cartoon series is a veritable trash compactor of familiar tropes and effects, borrowing from movies and graphic novels and anime and videogames(sic)."
This may not look that harsh, but "trash compactor" doesn't seem like a very friendly simile to me.
As for some of the choices here, I think The Boondocks deserve a listing. I can't think of an animated sitcom that uses the animation medium to its effect better, aside from maybe Drawn Together, which was a mess in practically every other regard. But for Boondocks, the frame rate is incredible and the designs have vigor to them. They may be "anime-esque", but in motion, the characters have great character. The fight scenes especially look fantastic. Not to mention that it's a genuinely funny show. I wouldn't rank it too high, but there are lesser choices for a list like this.
Archer is a show I'm loving to death now, but I don't know if I'd rank it here yet. I can see what happened with The Venture Brothers, a show I admired for similar reasons in its first two seasons but became too convoluted and raunchy for my liking later on, but for now, I'm in awe. The writing in general is what sells it for me. I love how unapologetically crass the show is, and that it can still handle intelligent the dialogue, how clever the plots, and especially how great the character development can be.
Sterling Archer is an incredibly oafish, chauvinistic lead, but he's so inexplicably likable( perhaps thank H. Jon Benjamin for that? He's really good at making jerks appealing, just by his expressions), and his relationship with his mother is brutal but distressing at the same time. I also dig the sexual tension between both Archer's relationship with Lana Kane, with Sterling and Lana's brief hints of lust and Malory's disapproval of her ability to please her son. The rest of the characters are entertaining as well, with a stellar voice cast, but it's the Archers and Kane that sell that show and make it worthy of making it among the greats, at least at some point.
Adventure Time, though, I'm not so sure I can defend. From what I've seen of the show, it's very creative, has solid characters, and clever designs, but the "awesome sauce" feel that the show pulls off and occasional wonkiness in it's scripts tends to get old. It even seems like the show's diehard fans from early on are losing interest as it goes along. The show's popular now, but will it be considered one of the best in a few years? It seec=ms like other popular Cartoon Network originals from recent years like Foster's, Chowder, and Flapjack are similar in that regard, as well. All are good shows, but I can think of about a half dozen other Cartoon Network originals that deserve to make it here instead of these.
And I'm also not so sure about Aqua Teen, Robot Chicken, or Liquid Television. Well, the latter had a lot of variety and ambition to share, but I'm not so sure if it belongs here. My other big beef comes with Ren & Stimpy, which I think gets more credit and hype than it deserves, but critics seem to love it regardless.
Everything else seems to fit in fine. I'm not a huge fan of Scooby-Doo or SpongeBob SquarePants, but both have left an undeniable impression on the pop culture landscape and on fans that nothing I can say can change. I also wouldn't consider Rugrats for a list like this, at least this high, but the first few seasons are quality, and it broke a couple of records that SpongeBob or any other children's cartoon haven't been able to reach yet.
But the rest seem to fit in fine. Some have undoubtably made a positive impact on the animation landscape, like the Looney Tunes (which got my vote under the incarnation chosen here), The Flintstones, and Batman: TAS, others are welcome and obvious additons, like the Groening shows, Animaniacs, and King of the Hill, and some just have all the reason in the world to appear, like South Park and Family Guy.
I'd like to have seen another anime or two make it on here, but Cowboy Bebop was a dame fine representation on here, and I'm glad that it's an option. In terms of mainstream success and overall quality, it really is the best of both worlds, and nothing else deserves to make it here more.
In hindsight, this is an imperfect selection, but given Entertainment's knack for choosing the most popular, recent options for it's lists, this wasn't so bad. And there are at least one or two shows that could have been ranked but I'm glad didn't make it in, so I at least give it some credit.
or 
for some people.
But very glad to see Genndy's "Clone Wars" on there. Which IMO is vastly superior to the newer Clone Wars series.