Soooooo...I'd like to say that something funny happened on my way to review these new chapters, but the simple truth is that I've been busy and I'm also a procrastinator so I really don't have any good excuses to offer. With that said, hopefully better late than never, so I'll get started with the criticisms and then move on from there.
"I'm concerned as well," Mami said. She pulled Nagisa up into a hug, and the little kid squeaked in surprise. Mami held the little girl close, burying her face in Nagisa's hair. "You've brought so much joy into my life, and I don't want to think about what might happen if you're not there once all this is over."
Something about the way this is worded struck me as off the first time I read it. This is only a minor nitpick and it flows better the second time, but I feel as though Mami (as hypocritical as it may be) should have said something about Nagisa's age and how it isn't safe for her to be there or what not.
I hesitated a moment, but nodded in acceptance. He was right, though I did not like that he was suffering so. But even still, how could I get past the dancers? There were too many, and no matter how I moved they followed and barred my path.
My shoulders slumped, and I was about to fall to my hands and knees when someone else came up softly behind me. It was another paper figure, but this one looked like me. She laid a gentle hand on my shoulder, and her painted lips were upturned in a quiet smile.
I think a slightly longer description (maybe another sentence or two?) of Madoka's efforts to get past the Clara Dolls might be called for here. The shift to her nearly falling to her hands and knees seems a bit sudden, and Madoka is not the type of person to give up on something easily.
"It's okay," I said. "Whatever it is, it doesn't matter. Everything will be all right?"
Shouldn't that last sentence end with an exclamation mark rather than a question mark?
Madoka's chapter also felt slightly perfunctory to me in terms of the flow from one action and development to the next, though that might be because I'd read the draft and knew what to expect. If you have the time and inclination, you might want to take a second look at the chapter and see if there are any places where you can liven up and strengthen the metaphorical connective tissues between paragraphs and scenes, but overall the chapter holds together coherently enough and (as I stated above) I suspect my perspective is skewed here.
Anyway, those are pretty much my only criticisms of note. I have my own opinions concerning Homura's motivations and reasoning that don't necessarily match what you presented here, but I can understand your own perspective and if I let alternative character interpretations get in the way of enjoying a good story virtually the only fan fics I'd like would be my own...and that would be terrible since I'm such a slow writer.
Focusing on the many positives, Kyoko's chapter was excellent. You wrote her POV with so much energy and gusto I'm surprised that there seems to have been a genuine possibility her narrative wouldn't have been featured in the story. That would have been a loss, in my opinion, as your depiction of Kyoko was so compelling and genuinely fun to read it nearly overshadowed Madoka in the climax.
Madoka's journey through the darkness with Lucifer was the highlight of her own chapter, and I like how you altered the scene with the Clara Dolls. Having them dance around Madoka was a clever reference to their Nutcracker Suite theme and a neat callback to Homura dancing at the start of the story.
Homura's concluding installment was very well written (possibly one of the best written installments in the story), and offered many thoughtful insights. Your take on Death was interesting and fits with what little exposure I've had to the character, and her placing Homura's hand in Madoka's was a truly heartwarming moment (and possibly necessary too, considering Homura had mucked things up badly enough that her soul might have been outside the Law of Cycles). As a piece of advice, though, I'd recommend putting Homura's installment with Madoka's in the archived version because it feels too short to be a chapter on its own.
And then there's the epilogue. I see there's been some discussion about chapter order, and I personally agree with GoukaRyuu, Ardion, and the others who feel that Lucifer and Madoka's meeting makes a satisfying bookend to the story. Putting this before Homura's meeting with Death would have had me scratching my head wondering why Madoka seems so calm and composed despite Homura's apparent demise.
Moreover, it offers an enjoyable resolution. Almost since I read the first chapter, I had wondered what Lucifer's role in this story would be: a mere catalyst who comes and goes without any changes to himself, or would he gain something from this experience? He's still the same person at the end as he was in the beginning, but I feel as though he's richer because of what he went through and the people he met. So, well done on your part in managing to portray this while keeping Lucifer true to himself.
And that's that, I suppose. Thanks for seeing this idea through to its conclusion and sharing the results with all of us. I very much enjoyed reading this and plan on adding it to my favorites over at Fanfiction.net.