Perhaps we're ranking based on a completely different requirement then.
I can definitely name animes that had better animation, artwork, style, presentation, music, dialog, plot, consistency, etc etc than Code Geass.
But why do we watch anime? Because its fun, and because its interesting. Even if you make an anime and make everything flawlessly, if you're not getting a huge kick out of watching it, it failed.
Code Geass gave everyone, or at least most everyone who watched it, a blast. And yes, Darker than Black season 1 was a huge blast, and season 2 ruined it for me.
I'm willing to place FMA brotherhood pretty high up on the rank too. Fun, interesting, great animation, good music, solid plot.
Anyways, I don't really feel like arguing which is the best, and like I said I only consider it one of the best and can only think of it off the top of my head. But if I had to make a list of "must watch" animes for all anime lovers, I'd put Code Geass in there.
Elfen Lied? Maybe in a different list. Its a fantastic series but doesn't appeal to the general audience. But DEFINITELY put it down for "must read the manga because its one of those animes that got altered and shortened".
Thing is, if my criteria for great series were based solely on whether they were "fun" or "not fun," then there'd be a lot of great series. But that's too small a scale for properly rating something, and not every series is based on its fun factor. There's also the case that there are series that don't affect me either way, but aren't necessarily "not fun." Take Monster, for instance. I enjoyed that series immensely, but the first adjective I would think of in pitching it to someone else would certainly not be fun. I also dislike the idea of ignoring all the flaws, small or large, in a series solely because it was entertaining. I feel that more or less sends the message that people want more of the same. No improvement, no innovation.
Over the past few years, it's become harder and harder to look at the seasonal lists and find something interesting to watch that isn't a season 2 of some show or more of the same in a particular genre. And I don't mean that in the sense that there's no such thing as an original story; I mean that in the sense that joke for joke, trope for trope, anime more than ever is becoming saturated with formulaic stories devoid of creativity. This problem has been around for years, but it's even worse now, when anything fresh is usually either someone trying too hard or not trying hard enough. Code Geass was a blast, but being over-the-top and turn-your-brain-off goodness shouldn't be the sole standard in a medium that's trying to convince people to take it seriously. All I've seen from Sunrise since Code Geass is that they're intent on replicating good Gundam SEEDs, but nothing else. Not everyone can keep trying to recreate Digimon: The Movie and eventually end up with Summer Wars. Most rehashes usually end up just as disappointing as, if not more so than the last.
When do we stop giving mediocre series a pass just "because it's anime?" When do fans of a series start giving real thought to why they like said series and whether or not their thoughts still hold up after dissecting it? I've long since moved past the phase where I liked anime series just because they were anime or because they were from Japan, and am now becoming acutely aware of what I like and dislike about what I watch and whether or not I'd consider said show a success or failure, much like I would with anything else I watch, read, or play. I would honestly have loved to see season 2 of Pumpkin Scissors air at any point during the past 4 years. Instead I have to facepalm at the notion that MM! gets a second season.
I don't enjoy writing walls of text describing why I like or dislike something, but I know I need to provide reasons behind my stance (and believe me, the bases I covered aren't even the tip of the iceberg for why I deplore this show) besides just saying "It's my opinion." To that, I ask, why do you find Elfen Lied a fantastic series once you get past the aesthetics, music and atmosphere and start looking at the heart of any series--the characters and/or the plot? Is there really something there you're seeing, or are you simply making a conscious choice not to look?