Kyubey knows about the Time Reset Homura lives.
Why? I think I remember in ep8 he tells Homura it's useless to try to kill him eventhough she tried twice. Also, he's able to understand Homura's power only because he remembers the first time she tried and begins analysing and making comparisons.
It seems KB's only power is the wish, he doesn't know which powers the MG will get, only that there's sometimes a relation with the wish.
My guess is that KB benefits from the reset. It might be possible KB can extract entropy in each loop. And in each loop it seems Madoka's bursts are stronger. That would be really mean to Homura of course, as she would be in fact the best ally KB could ever get in his quest.

Truly a nice episode. I admitt I've been surprised by that show, I didn't think I would like it, but I do, and for very nice reasons like a good scenario if you forget KB's origins