[Spoiler (click to open)]The reveals in this episode were, pardon my French, fucking amazing. Magical girls grow into witches, faster if they give into despair faster; Kyuubey is short for Incubator - for the magical girls' souls? He's referred to Grief Seeds as witch eggs, and since Soul Gems become Grief Seeds when darkened by magic use and despair, that makes the most sense.
Also... huh. A killed witch drops a Grief Seed, which (after being used to stave off the magical girl's transformation) Kyuubey takes, "eats", and... what, incubates until it's ready to become a witch again? Geez, this whole system is a losing battle. There's always going to be more witches than magical girls, so long as Kyuubey is there to incubate the recovered Grief Seeds. But without Kyuubey, odds are that they'll run out of magical girls to fight the remaining witches (especially if familiars can become witches on their own, further contributing to the imbalance), and the world will fall into despair.
The only way Kyuubey can even remotely be potentially considered not pure evil is if the first witches were these evolved familiars. Then the magical girls are a failing defense, probably because of some rule of the universe Kyuubey's powers can't overcome (but Madoka's could?), but without that defense the world would be doomed. So what Kyuubey does would be twisted and wrong, but with good intentions behind it.
Not that I have problems with Kyuubey being pure evil, mind you. As best I can tell at this point, it's equally likely that he wants the world consumed by witches/despair. I just like considering morally gray possibilities. (I, for example, can totally see Kyuubey's logic in keeping one's soul outside one's body. That may've been abhorrent to Sayaka, and been the trigger point for her downfall, but it wouldn't have bothered me.)
Homura being from another timeline wasn't a surprise to me; honestly, it was a moment of pure vindication. (If you follow me on twitter, you know I've been speculating about time travel-related shenanigans with respect to Homura for aaaages.)
But I don't think she got to this timeline from her home timeline. I think there were several botched attempts at fixing... whatever she's here to fix (Madoka's death? Madoka's magical girl wish? whatever's going to happen on Walpurgisnacht?) before she got to this timeline. And, funnily enough, the reason I think that is because of Groundhog's Day and "Mystery Spot" AU fics.
Homura's characterization - the aloof, distanced nature, the seeming omniscience (if not outright omnipotence, early on), the certainty that some things will happen at certain times and places, equal certainty and determination that other possibilities must be avoided no matter what - reminds me of how characters aware of being caught in a time loop act, towards the end. For a lot of minor moments, they're just going through the motions, no feeling behind it, just doing what needs to be done to get people to do what they would've done anyway. As they get closer to the major (often traumatic) event they're meant to change, they lose that emotional distance, get more and more frustrated with the people they're trying to save, especially if they're unable or unwilling to reveal that they're in a time loop... basically exactly how Homura started losing it when Madoka tried to make a contract with Kyuubey in this episode.
It's fascinating, seeing this pattern of behavior in a character I'm meeting for the first time long after she starts time traveling with purpose.
It also makes me hope there's Groundhog's Day AUs out there for Homura and Madoka in a less traumatic, more mundane context.