If "A potion spends that which is invested in the creation of its ingredients." then what the heck goes into an Animagus potion? Something that's been transfigured a lot?

Edit: It doesn't seem like the method for becoming an Animagus is described in canon, so the potion aspect might be new to MoR.

Harry with the ability to invent potions would be powerful enough to wreck the story.

Harry with time travel would be enough to wreak the story. Harry with an invisibility cloak would be enough to wreak the story, Hell, harry with rationality would be enough to wreak the story.

That is, unless the other obstacles were ramped up to deal with it. Give Harry a time turner and enemies clever enough to know how to check on him. Give harry an invisibility cloak but add spells that can detect the presence of a deathly hallow. Give Harry mastery of potions but make creating them slow or just plain difficult.

Worse? What makes you say that? We seem to be seeing ever more action on his part, I actually would have said: from the Azkaban duel to his commentary in battles (and setting them up too) to his casual displays of sheer power/skill in the interrogation of chapter the last.

I'm puzzled by Harry's sunlight potion. Did it not require a magical ingredient?

Since we are told that there are no magical ingredients in the lesser woods where the battles are fought, and that all the potions in the books that Harry looks through unlock and redistribute magical energy (rather than ostensibly non-magical energy like sunlight), does this mean that Harry discovered a way to brew potions without magical ingredients? I recall no hint that this is possible, and yet no one watching the battle seems to find the potion notable. To be fair, the fundamental potion-making law doesn't explicitly rule out an all-mundane potion ("A potion spends that which is invested in the creation of its ingredients").

I also find it unlikely that Harry invented the potion himself (I believe general potions-theory and the system for deducing the proper arbitrary stirring patterns would have been given a more complete coverage, if that were the case), so it appears that Harry found a suitable potion using Flitwick's recommended resources. But I still don't know whether the "magical ingredient requirement" is absolute (and Harry bypassed it just by, e.g., putting something of his own magic into the potion as a trigger but not as the main ingredient), whether it's a mere conceptual limit that wizards never thought to test, or whether potions with non-magical ingredients exist and are well-known, but are relatively so rare that Harry just didn't happen to run across any in his initial search.

What am I missing?

Everybody sleeps eventually, which is worse than Quirrel's catatonia.

(Can't find a good place to insert my entire current edifice of theory elsewhere, so I'll put it as a top level comment.)

Quirrell is Voldemort is Mr. Hat and Cloak. Quirrell's ultimate goal is driving Harry permanently into his Dark Side, so as to be another Voldemort, either to rule alongside the real Voldie or to be led by the real Voldie.

Quirrell's first attempt at driving Harry over to his Dark Side was with the Dementor in the Humanism sequence. He would have succeeded, had Hermione not been there to bring him out of it. So from Quirrell's point of view, Hermione is Harry's anchor to his good side.

So then it makes perfect sense for all the events of Self Actualization and this new sequence to be Quirrel/Voldie/H&C's handiwork. Quirrell helped SPHEW win that last battle in Chapter 74 so as to paint a larger target on Hermione. When Harry came to him with his plan for that battle, he just laughed, because Harry had unknowingly come to him with a brilliant plan to further Quirrell's own goals for Hermione's doom. He poisoned Hermione against Draco (which was difficult, because Quirrell is pure evil and Hermione is pure good and he can't understand her) so as to provoke House Malfoy further.

Now Hermione is in deep trouble, just as Quirrell intended. All that remains is for something unspeakably awful to happen to her soon, which, Quirrell believes, will help do to Harry what the Dementor almost did in January.

Hat-and-Cloak is Voldemort but not Quirrell. When in Quirrell, Voldemort has a whole (probably quite powerful!) brain to run his computation on. Outside of Quirrell, he relies only on what computation he can do purely as a 'ghost', or as magic, or whatever. Hat-and-Cloak is thusly disguised because Voldemort lacks a body. Or maybe Voldemort possesses someone else, who isn't as smart as Quirrell, and is proportionally dumber and more prone to mistakes. Quirrell is zombie while Voldemort's away because Voldemort set it up that way. Don't want your robot walking away without you.

Part of the groundhog-day attack involved setting up a trigger in Hermione, that when she can attack Malfoy, she should try to kill him. This explains her behaviour in the battle, and her apparent behaviour in the duel.

Hat-and-Cloak is a player in this story. Players in this story are clever and powerful. A sensible way of resolving this apparent contradiction is to postulate some form of disability or restriction applying to Hat-and-Cloak. Then all you need is Conservation of Characters.

Hermione probably won't be cut off from any outside contact, so she will be able to tell Harry about the duel if she wants to/is able to. We can't discount the possibility of obvliation.

I think you're reading too much into it. Mysterious makes sense when you're describing a feint.

I wouldn't say that H&C is necessarily new to the concept of Groundhog Day Attacks. If Quirrell is Voldemort and also H&C, he would not likely have a good mental model of the pure and innocent and good and upright Hermione Granger. It would take him a few tries to find the right levers to push.

But I'm not sure that Hermione isn't simply under the Imperius Curse at this point. When she's fighting Draco, she gives her wand a "mysterious flick" in a very un-Hermione-like feint. I don't know why Eliezer would deliberately place that word "mysterious" there unless he wanted to hint that Hermione isn't fully in control of her faculties.