I realize that everything you say is true, but I feel like in the course of their deconstruction, they break a lot of story-telling laws that would have made the show a lot more enjoyable. I'm not saying it's "same old, same old" either, or at least I don't mean to--what I mean is that the tropes the turned to in the end, the Faustian bargain, are things that I'm used to and that enough of it was a dry old take that I wasn't too interested. Trust me, the show has a good feeling... it's a very good product. But so many scenes are things where I think "ah, I've seen this before" and then it's executed in exactly the same way. Simplicity has often been replaced with simplicity... the lessons given to us are, I feel, fairly in the water nowadays. The main difference I expect to see is that in most magical girl shows, these errors can be fixed. Here, I'm expecting some sort of tragedy.
(Let's be honest, I don't actually like anime. I like some anime shows. In the magical girl department I like Kamichama Karin, Card Captor Sakura, and Princess Tutu... and that's about it. Well, Revolutionary Girl Utena as well.)
The thing is, there are some very impressive scenes, like Mami having her head bitten off and Sayaka's soul gem getting tossed, or the first little bit with Homura (that her power is so very subdued and non-flashy... I was really pleased by that feature in contrast with Mami's enormous guns, and I do think that was a feature of a successful deconstruction--that power doesn't look like flash and display. Power is pragmatic). But I feel like they made some things too easy to anticipate. The labyrinths were creepy for a while, but they never did anything so shocking that I was overcome with a feeling of horror. Let's be honest, Mami's death could have been much worse. I feel like I may simply be too old to be the target audience, which is fine.
I think the ally/enemy question would have worked much better in a longer show, where more groups of characters could have been established. Sayaka and Kyoko become allies to each other at the end of one backstory-establishing scene, which I felt was dissatisfying. The characters are flat enough that I can't get a good understanding of them.
Evangelion works because the show is established through a very spiteful relationship between Shinji and his father. Shinji may spend most of his time being passive, but he's passive-aggressive and there is constant tension--between them, towards women in general, towards his friends who initially were his bullies. Because Homura and Madoka don't know each other, there honestly isn't that much tension built up, and to the best of my knowledge the two of them have the main friendly relationship in the show. I would have liked to have seen it be more antagonistic, so any friendship would be more satisfying later on.
I guess this is what I'm trying to say. Throughout this show, I find myself unconcerned with Madoka. She spends a lot of time crying, but most of the time she looks fine. I'm not feeling her misery. The first episode's conceit hasn't been mentioned or dealt with since. Where is the main source of tension? It shifts, it moves around... first with Homura, then with the witches in general, then with Kyoko, then between Sayaka and the gal who steals Kyosuke (barely), then with Kyubey. I feel like the show is poorly-focused.
The fact that the girls can't be physically damaged also sort of removes some of the tension, I've got to be honest. I understand that they're trying to keep one of the tropes up with an unexpected twist, but something else would have worked better for me.
I like that Madoka's decision is held off, but I feel like it isn't a decision she's making herself--it's held off to be examined, but doesn't get much examination. I don't see much of an internal struggle. It's a choice that Homura persistently makes for her, but refuses to explain (that had better get some lip service). Madoka wants to become a magical girl, Homura stops her, there's no pursuant psychological breakdown or increasing antagonism towards Homura as the choice she's refusing to make becomes more and more important. It's not a personal thing. It's just a thing that keeps happening, and Homura can pretty much always save the day anyway, so it sort of doesn't matter.