Currently Airing Anime

Very minor detail, but

 Spoiler

In this episode Homura's hard outter shell gradually cracked open. The whole episode she didn't refer to Madoka by her full name, like she used to do and like she still does with everyone else. She still says "Miki Sayaka" but not "Kaname Madoka", she just says "Madoka" now.

 Spoiler

Did you noticed what Homura called Kyubey?

"Incubator"

Is that hinting at something here?

Of course.

 Spoiler

Kyubey's job is to incubate witch egglings (magical girls). He doesn't only collect the sins from the grief seeds, but he continues the cycle of creating new witches. The Soul Gem can be thought of as a witch egg, it even bursts open when it "hatches".

[spoiuler]
I guess everything up until this point has been correct. Homura does have time-manipulation powers, and she's from another timeline. The hints that SHAFT's been pushing up the ass have been helping us a lot at this point. My question is, what is Homura planning on doing at this point? Kyubey's objective has been hinted too.

Also, I noticed how Homura said 'something' was coming, but since Sayaka's soul was cursed, it's going to be another obstacle for them or something like that. So I'm now wondering on whether Sayaka is transforming into that being we saw in the 1st episode, or not. But I don't think it's the same witch, because the witch at episode 1 looks obnoxiously powerful and large. I don't think Sayaka could be that witch, unless SHAFT's in a major rush to end the series now. I'm also wondering if Madoka is going to become a Magical Girl..

 Spoiler

I'm too lazy to dig up the stuff now, but there are several convinient simularities between the witch's design in EP 1 and Sayaka's Magil Girl uniform, including that cresent moon she has. You can find it on Madoka wiki, but pretty much since EP 1 it's been speculated that the witch was actually Sayaka because someone looked at the concept art for Sayaka's magic outfit and compared it to the witch.

 Spoiler

If she does, then she's only doing so because she feels guilty for Sayaka's transformation. Or if she doesn't, will she still worry about her friends? So many questions, so little time. Series is coming to an end shortly. 4 episodes left if it's a typical 12 episodes series. SHAFT has to be continuing this, otherwise, we'd be missing out on too much information.

Who knows. The spinoff manga may go more into depth on some stuff the main series skimmed over.