Considering the recent revelations in ep. 9 of Madoka Magica, just getting rid of Kyubei might not be enough, or even more difficult than just that.
Turns out that Kyubei is representing one or more
Sufficiently Advanced Alien civilizations/cultures who wish to exploit the magical girl-->witch transformations for infinite free energy. He probably just doesn't seem all that powerful due to saving energy, more than anything. In any case, it's very likely that his kind
is powerful. Though I hope not so powerful as to be beyond a SuperWitch!Madoka's reach, as a SuperWitch!Madoka-goes-Unicron-on-their-ass end is probably the best we can hope for in the show at this point. Anyway, fighting them, depending on how the show portrays them in the next 3 episodes (if it does at all), could be a huge challenge for Zeke--it gives you, potentially, some pretty frightening antagonists to use.
That said, it seems like the
biggest problems are the failings of the magical girls themselves. Every single one of them that's bit it/fallen so far has done so due to their own personal failings.
Yes, even Mami. She absolutely refused to extend Homura any trust, who, granted, is not really the best with people--but even so. Even if she had simply compromised and, still refusing to just leave it to Homura, had allowed Homura to come along (NOT binding her on the spot), she'd probably still be alive.
From what I've read, I think Zeke might make a seriously positive mentor. So might the Senshi, for that matter--though I'm not sure how Puella Magi Madoka Magica style magical girls would react to the Senshi (specifically to learning that
--might be a
teeny bit of resentment/jealousy there).
Sorry for all the spoiler tags, but, well, spoilery spoilers are spoilery.
Two great tastes that go great together!
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Spoiler