I've been meaning to rewatch Puella Magi Madoka Magica more or less since the instant I first finished the series. Haven't yet found the time - I've only got it on Blu-ray, and need to take up the living room to watch it - but something about it occurred to me this morning, which disappointed me the first time through even though I wasn't really sure what it was.
Basically, it's not enough like Evangelion. Bear with me.
To begin with, Eva is so full of clichés and homages and Giant Robot tropes that the audience is left with a particular expectation. That initial setup is mostly delivered for the first few episodes, with the darker psychology and conspiracy stuff creeping in around the edges1.
By contrast, the very first scene in Madoka is thumping Yuki Kajiura techno and dark imagery and it's immediately obvious that there's more going on than the main character realises. It doesn't set up any false expectation; having an episode or two of sugar and laughs building up to the sudden and traumatic [spoiler goes here] would have given the whole show a twist that it's sorely lacking.
Then there's the closing episodes where the reasons for Kyubei recruiting Magical Girls are a bit predictable and over-explained, and the ending's kind of... well, bad. Hopefully the movies will wrap things up more completely, but I'm not holding out much hope.
1 The best episode of Evangelion, for my money, is Both of You, Dance Like You Want to Win!; I've always been disappointed that Shinji and Asuka's relationship never seemed to evolve despite the episode finishing with them as equals. But then, Anno's overarching story might not have worked (your mileage may vary whether you think it did or not).