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SPOILERS UP TO PUELLA MAGI MADOKA MAGICA EPISODE 9
Today I finally finished all the Madoka episodes that have aired this season. I enjoy the series; it can get quite deep at times and the characters are well developed and likable. I'm not sure exactly how good this anime will be when it ends, but right now it's among my favorites. However, among other flaws, the latest episode finally revealed the motives behind Kyubey creating magical girls in the first place, and wow, it made me die a little inside. I wrote most of this out on a forum, but I'll add a little bit more detail and structure my thoughts more clearly.
Kyubey fails physics forever. His explanation for creating magical girls out of humans is that the energy they create resolves the issue of entropy in the universe. However, Kyubey doesn't seem to understand entropy correctly. The concept of entropy does not state that energy is gradually lost over time, but that energy becomes less useful over time (a subtle but important distinction). He (well, technically IT but I'll use the masculine pronoun for convenience when referring to Kyubey) cites the second law of thermodynamics as the reason for this phenomenon (which he incorrectly interprets). Besides, what laws of thermodynamics are they following? They must obey the second law but completely ignore the first? Also, what's to say that the energy "created" by Puella Magi can be harnessed without increasing entropy as stated by the second law? Incubators must put equal work into the system in order to harness and store the free energy of witches, thus canceling any potential benefit. I guess one could argue that incubators have the capability to store free energy through their work (like charging a battery) but not create it, but that still does not explain how the energy is harnessed without the expenditure of energy. It's junk-science and it ticks me off that it's said in such a serious context, not to mention acts as the foundation of the antagonist's motivation. And another thing, entropy works on a scale of BILLIONS OF YEARS, and yet Kyubey acts like the universe is running out of energy like fossil fuels on Earth. And unless the power of human emotion has the power likened to that of several star systems (because the entropy caused by the dissipation of solar energy is what largely needs to be rectified right?), I doubt the energy harnessed would make a significant difference anyway. If it is on the level required to rectify the entropy of the universe, especially since the energy is meant to exist in "higher dimensions," the concentration of energy should rip apart the fabric of space time whenever a grief seed shows up, thus ending the world as we know it even before the Puella Magi get a chance to battle it.
tl;dr: If the writers mean "magic" they should just say "magic" without framing it into a crappy physics explanation.
I probably made some mistakes of my own in my physics analysis, so feel free to call me out on any errors I made. Still, there are obvious flaws in this motive that seem to contradict the very physical laws that rationalize the motive.
Edit: SPOILERS FOR EPISODE 10!
Only a couple of small adendums here. First is a shamelessly stolen tvTropes explanation.
tl;dr: If you just throw science out the window and unlearn what you've learned, it's actually a pretty good explanation. However, if the writers wish to work within the bounds of science for some justifications and outside for others, that's not good. Bending science to your will is just a sign of not doing research and being lazy.
Also, there are two images from the new episode that I wish to talk about. This one suggests that it is not the power of the magical girl but the wish itself that causes the shift in entropy. I actually put this as a point towards pausibility, as it brings it further detached from the science it mangled so horribly. However, this one breaks my heart. We're talking about the ENTROPY OF THE UNIVERSE HERE! There's no freaking way that one person could contain that much energy without destroying the time space continuum. No way.
To conclude though, I'll quote what I said on an internet forum:
I don't care so much about Kyubey's crazy explanation. I don't care about the linearness and predictability of the earlier episodes. In the end, it really doesn't matter what Kyubey's motive is. It takes a side stage to Homura's motive; fighting what seems to be an impossible puzzle. While I do believe that the anime will have a downer ending, I wouldn't mind if she did find a way out. This is quickly becoming one of my favorite anime of all time. My favorite anime are not judged by their technical excellence, but their excellence as art, and Madoka epitomizes that standard.
I might be a slowpoke here, but I just found out that the Know Your Meme page for Kyubey links this blog. I feel rather accomplished now.
Response to ZetaAspect:
Firstly, I'd like to applaud you for finally calling me out. I was getting uncomfortable that my pseudo-physics analysis was not getting any opposition. In fact, as I stated, I did not want Kyubey to be wrong. In fact, I wanted to come up with some explanation, however implausible, that would make sense in the context of the anime (e.g. resolving endings like Clannad AS and Angel Beats, which are much messier than Madoka).
The reason I object to his explanation of the first law of thermodynamics is that it isn't just a simplification, but a justification for the main physics breaking principles in the anime. If one makes the assumption that energy can be "lost," then the fact that energy can be "created" out of emotion is not a far stretch. This, as you stated, probably should have been my focus, although looking back it is quite silly to point out "the power of love" as a violation of the laws of physics.
You make a very good point regarding the role of incubators. I had misunderstood how they function in the energy "creation" process. There would be no more work involved than that involving a rechargeable battery regaining power.
I was under the impression that humans were the only emotion capable beings in the Madoka universe, thus why Kyubey and the other incubators were on Earth. As for Madoka's energy potential and the implications of that, I suppose one can 1. assume that the time loop occurred MANY more times than was shown in the series (like with Endless Eight) and 2. that witches appearances WERE disturbances in the time space continuum, although not to the scale of tearing apart the universe (since in each "loop" Madoka's energy was not at dangerous levels).
Now, I love science fiction, but even then I call out times when the writers get science "wrong." You're right that writers have license to "invent" scientific principles (e.g. "subspace" in Star Trek or "emotional energy" in Madoka), however, I thoroughly enjoy it when these "inventions" work within the context of the laws of physics as we know them. Honestly, now that I'm reevaluating this problem, I don't think the writers even NEEDED to "change" the laws of physics that much, if they simply attributed more to "magic." Again, this was too high of an expectation from a series not targeted towards physics gurus (myself not included, obviously :P)
And of course, collection quotas can be within a certain "time" period (then again, what is time in this series?), and Kyubey's line did not imply that the problem was "solved," otherwise, he would have stopped collecting energy from the magical girls and found a way to release them.
Summary: He still fails, but less than I thought he had, and certainly less than he needed to.