Madoka:
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I was very suprised by Madoka's wish: "KILL THEM ALL!!!" Like, if you're rewriting the laws of the universe, couldn't you go for a less bloodthirsty solution like solving entropy or simply making soul gems uncorruptible?
Also no comments on the fact that Homura herself seems to be descending into madness while ascending into some kind of Neo-Witch just like Madoka evolved into Neo-Puella-Magi? That's totally calling for a 2nd season of the series!
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Regarding the wish, there are still limits based on power(you would need infinite power to solve entropy by rewriting the universe I think), and Madoka is by no means unaware of the nature of wishes. Since she had only a few days to think over it, rather than risk causing more problems by trying to solve it all(end entropy, the Incubators never came to Earth, mankind in stone age or Perfect Soulgems, which could take any of a million possible iterations), she wished to have the ability to solve one specific problem.
Hence why the "by my own hand" line. She will personally save each and every girl from the brink of despair in the exact way she wants(as opposed to ending all Witches by making them all drop dead, killing all magical girls in the same stroke, or making soulgems incorruptible by petrifying all girls through the ages as soon as they make their wish).
So they make their wish, fight their battles and at the end of life Madoka takes them personally to Valhalla. Note that girls no longer become Witches because their soulgems darken from despair, but they CAN run out of energy and the despair simply manifests external to them anyway. Running out of energy of course, kills you when you're effectively an energy being. Not bad for a wish she had less than a week to think over, as a teenaged girl. Maybe she could have done better, but it'd take a lawyer-philosopher quite a while to work out a 'perfect' wish.
As for that last, her battles come to an end, she wants to see Madoka one last time. Me, I like leaning on the Madoka-Valhalla option. Where else should 'disappeared' magical girls go, than the formless realm she is in?
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