1 And so, what bugs me is: why Nessa? Which I guess is the key to series.  A doppel for the series of clones, or perhaps she's the one true key and the clones are merely attempts to create her/it? 

I do like this series, even with its meanderings.  I'm glad that the malformed doppels from the beginning of the series didn't reappear, though.  I found them so unappealing that I almost gave up on it, and I think I would have been sorry had I'd done so.   Clain is vaguely heroic enough to inspire believability and sympathy, and main Phryne's lack of physical awareness was well explained by this episode.

This series really would have stood out had there not been a Madoka Mahou Shoujo Zombie Level E Wandering Son Fantastic Yumekui Midriff series occurring at the exact same time.

2

Yeah, it isn't bad. But despite the director's hopes, it doesn't really stand out. As you say, this season has featured a surprising number of series which do break the mold. Madoka and Zombie both clearly surpass it.

Madoka in particular looks set to become a monumental achievement, ranking up there with Haibane Renmei in the pantheon of truly great series. Of course, we won't know for sure until it's over, but that's how I'm betting now.

3 Personally, Madoka? Not a fat chance. It's one of those anime that achieves notoriety by, frankly, shocking. It's not like it's not ridden with clichés, its substance feels like eating cotton candy, and it has that snobby attitude that because it broke a genre it has created a new (and better) one.Yeah, popular right now but I doubt it will pass the test of time, like Astro Boy and Dragon Ball, for example. It's the same with Fractale; like it happened to me with FMA, interesting set up and made me expect good things, and then.... sigh (in FMA's case was pure disgust). I'm truly getting wearied of this "plot-turning revelation"; Evangelion was even the first one to use it, but being the epitome of it, after a decade it's starting to shake as well. I don't think it's gonna survive the test of time either.

4 I disagree--your objection seems flimsy.  Plot-turning revelations are cliché now?  Plots can only follow straight line paths from beginning to end, without any "game-changers"?   Ridiculous.  You claim it's overused by animé, but I have to point out that it was probably old when Shakespeare was penning his first play.  It's not the device -- it's the execution.

It's not just that Madoka is turning everything on it's ear.  It's how well it is doing it.  Just the right amount of foreshadowing.  No wasted moments in storytelling.  Believable characters. A truly terrifying villain, not because he's vicious, violent, or malevolent  -- he's none of those; he's just got a plan that doesn't take into account the collateral damage it causes.

I don't know if I'd hold it up to Haibane Renmei status, but this series is not a flash-in-the pan.  It's one we'll be looking back at as a classic for some time.

5 I don't really see what is so shocking about Madoka. It sounds more or less like it is the series that I've been waiting for the Japanese to make for some time. When I watch maho shojo, at times a part of me suspects things. As far as I can tell, except for having a secular villain, Madoka is a series where these suspicions would be true. I'm not sure at all that I want to see it. I don't know that I'd want to see a story that fit my expectations on these matters well enough to have a satisfying end. As it is, Madoka has a wider potential market than it would have by chasing my expectations the rest of the way, and doesn't seem to be running the risk of becoming a maho shojo Jack Chick either.

I want to say that Homer used that device, but Homer is still young compared to some extant writings, and I don't know his stories well enough.

I'm too much of a moron to have anything to say about significance. I haven't seen any of this season's anime. My second best (would be first if my process was saner) rated anime for this season is the Drucker one, purely because of the incredible potential it has for nonsensical fanfics. (Even if they've already made an anime of "An ordinary highschool female extraterrestrial reads Dan Simmons' Hyperion Cantos".)