Repo! The Genetic Opera/WMG

Rotti's illness is leukemia.
It's implied to be some form of cancer by the doctor at the beginning saying that it's spreading and the scene where it's shown that he wears a wig, and blood is just about the only thing that we never see or hear even a hint about GeneCo being able to replace it. It would also make let his illness echo Shilo's and Marni's, and the "your designer heart still beats with common blood" line in 21st Century Cure could be a hint towards it.
 * Alternately, Rotti's illness is AIDS. It would explain the lesions he's trying to cover, also.
 * I think the "Your designer heart still beats with common blood" was a reference to the fact that the corpse he was extracting the Zydrate from was that of the girl killed-and-cardiectomized at the beggining of the movie by the repo man

Out of all of Shilo's medicine, only the fizzing blue stuff which was diluted into water was .
The movie makes a point of showing Nathan preparing it for Shilo when she was being or had just done something especially rebellious, even if her medicine alert wasn't going off, and they always focus a lot more on her drinking it than they do on her taking her pills (Alexa even complains at one point in the commentaries about how they'd keep the camera focused on her until she'd chugged the whole glass down). All the rest of her medicines are there to

Inspired by the above WMG, Shilo's blue medicine is actually Zydrate.
It's blue, it, while in certain outside the movie material Zydrate is said to. Whenever she missed her medication and fainted, she was having withdrawal symptoms.

Zydrate WMGs

 * Zydrate caused the organ failure epidemic.
 * Zydrate is produced by the bacteria that caused the organ failure epidemic (like how botox is diluted botulism toxin).
 * In either of those two cases the Graverobber would have been extracting it from plague victims (or regular GeneCo customers).
 * Zydrate is a natural neurochemical, but extracting it destroys the brain in the process.
 * Which explains the needle up the nose, GeneCo probably uses artificial brains to produce it.
 * The only corpses from which street Zydrate can be extracted are former GeneCo customers (or former Graverobber customers) because it naturally accumulates in the brain fluid and does not degrade over time or after death.
 * Zydrate emits gas around the area where it is injected, which causes a radial effect in the area causing everyone present to receive a mindfuck like the one in the middle of Zydrate Anatomy.

Nathan was given Super Soldier enhancements as part of his job
He took out multiple armed and armored soldiers with nothing more than scalpels, he only fell when his beloved daughter was present.

Rotti is Shilo's father.
As was mentioned on the main page, both of Marni's relationships took place seventeen years ago. This proves that Marni's marriage to Nathan likely spanned less than a year (her death having occurred 9 months or less later). If she had been pregnant before the two were married, it would have been difficult to tell who the baby belonged to. It's also pretty noteworthy that Rotti seems oddly attached to Shilo. Just because she's his ex-girlfriend's daughter? It seems a trifle suspicious if you think about it (in a non-squicky way, of course.)

Repo takes place in the same world as the Casshern movie.
In both, nature has been almost completely wiped out and people's organic bodies are beginning to fail as a result. They even look kinda similar, aside from Casshern's retro-Imperial Japan bits.
 * By extension, the reason Nathan's so tough is that he's got a Shinzo Ningen body imported from Japan.

Nathan is a descendant of Sweeney Todd.
I know this is a long shot but...just look at how he look at his scalpel in the "Night Surgeon"! And how he just seems to have a natural talent for slicing people open, not to mention his sick sense of humor (his, er...ventriloquism act) and quest for vengeance towards the end.
 * What sense of humor? The closest thing Mr. Todd had to a sense of humor was a flair for punning (when prompted), and arguably the "looks like a duck, acts like a duck, tastes like a duck, it's a duck" bit regarding Pirelli's elixir.

Graverobber is Louis.
Because they look similar (at least the present-time version of Louis does). The premise of the guess assumes that Graverobber isn't wearing makeup and doesn't look like that because of drugs (unless you count "vampiric blood withdrawal" as a drug-related effect, and "human blood" as a drug). Louis worked on getting a friendlier accent, since potential customers and young runaways who may or may not also be potential customers need to be more at ease than an interviewer.

Graverobber is a Fourth Wall Observer.
He narrates and exposits because he can tell where the cameras are (whether they're real or not), and the screaming in the graveyard was because he's a Large Ham and "knew" that he would escape (at least eventually).
 * The Cardboard Prison idea is unlikely since the signs said that graverobbers would be killed on sight.

Related to the above WMG: You can't see the fourth wall when you're upside down.
Graverobber always seems pretty confident about where the plot should go next--explaining Zydrate and Blind Mag's contract to Shilo for no apparent reason other than exposition--the only time he seems clueless or uncertain is during the cut song Needle Into a Bug.

Graverobber and Rotti Largo are related.
Graverobber has a vested interest in Shiloh - despite the fact that this interest seems to change (Early on, he screams and draws attention to them both, putting her in danger. Later, he safely escorts her away from the fair AND Largo's goons before and after Zydrate Anatomy). It's possible Graverobber was, in fact, one of Rotti's children, for some reason cast off. He seems older than Largo's other children (who already bring up questions of their own, as they all seem older than Shiloh). It's also possible Graverobber chose to turn against his father for some reason.

Graverobber and Marni are related.
Again based on Graverobber's attachment to Shiloh. It's possible Graverobber was in fact a son of Marni's, or even her brother (his age is rather hard to tell under all of the makeup, and we don't know too much about Marni's age either). The only problem with this is the fact that he attracts attention to her when he roars in 21st Century Cure, which seems counter-intuitive if this is the case unless he doesn't realize she is his half-sister until later.
 * About Marni's age, we do get to learn it as early as 8th minute into the movie. Her lifespan (2011-2040) is carved on her tombstone.

Graverobber is an anti-hero trying to destroy GeneCo.
This actually has a few points of evidence to it. First of all, there is the fact that he deals in underground Zydrate - which may or may not actually hurt GeneCo (some speculation on that is found in the Just Bugs Me page) but here we're assuming it does. As for the impact of 21st century cure, it's possible Graverobber knows Shiloh is the Repo Man's daughter and hoped she would be harmed, it's possible he knew she was the Repo Man's daughter and knew she would not be hurt because of it, it's possible he didn't care at all about her and simply needed to make a quick escape, it's possible he had suspicions and wanted to see what happens. In addition to that, when he sees Shiloh at the fair, he seems intent on showing her the darker side of GeneCo rather than the light-heartedness of the fair, and even provides exposition as to Mag's situation (knowing full well Shiloh's a fan by her recognition of the song). Then, he talks about having GeneCo undergo surgery at the very end, quite possibly hinting that he would keep messing with GeneCo now that it is under weaker management. One of the above two WMG's may apply as well.

Zydrate injections really do go against your anatomy.
Orifice Invasion. That's all I'm saying.

Shilo grows up to be a high-level Zydrate dealer in Graverobber's footsteps, while singing under the GeneCo license For The Art.
Shilo knows only two living people by the end of the movie, and the one that isn't Graverobber hates her. Even if Shilo can go back to her house without police intervention, it's possible that she cannot bring herself to do so. Considering, working for Graverobber and giving a new, more innocent face to his Zydrate business while singing under the GeneCo name might be the easiest way she can follow her dream of becoming a singer (and the easiest, least debasing way for her to make a living at all), if not the only way.

The Repo Men aren't really repossessing organs
They're after the extracellular matrixes. Hear me out, the few organs we've been able to grow from stem cells required the ECM "scaffold" of a pre-existing organ taken from a cadaver. Makes a lot more sense than trying to retransplant a whole organ without rejection.

The epidemic was only on one isolated island.
Like in Bioshock, the entire organ failure epidemic (Key word here! Epidemic. Epi = One. ONE island.) took place on one island. To stop this disease from spreading, the bridge connecting this island to the rest of the world was destroyed (As evidenced by the opening fly-through of the island). When Rotti says, "The World", he only means this one island, as it is the world to him and it's inhabitants. They have no way of getting off of the island, so this might as well be their entire world. No one would dare venture here, and many people have forgotten about it due to what it has become: A horrific nightmare of a city so narcisstic, consumerist, and just plain bat-shit insane that nobody dares even think of what is happening there.
 * There's no way an island covered in an urban cityscape could be self-sufficient; with no contact to the outside world, they would have no resources for energy and production, no raw materials (the GeneCo building didn't build itself, among other things) and no food to feed the population. The population would've been reduced to cannibalism and subsequently died from organ failures long before any of the set-up.
 * Who said Gene Co doesn't create artificial food? As for those other things, those are some pretty good points. Maybe it was magic.
 * Soylent Green?

Gene Co caused the organ failure epidemic.
The poison that Rotti gave to Marni seemed to cause her organs to start failing. It isn't too much of a stretch to imagine that Rotti introduced this poison elsewhere to cause the epidemic that rocketed him to a position of world domination. If you are running a business that produces organs, how else would you create demand?

Repo Men is simply a side story of a Gene Co customer.
Mostly for crack, but feel free to correct me on this though, considering I've yet to even see Repo Men. But thats what it's coming off as. Future of organs being a commodity and issues paying off the organs you bought.

Nathan Wallace's name used to be Noah Antwiler.
And, obviously, is what became of Dr. Insano.

The movie is the death-hallucination of Graverobber and Amber is the same person as Shilo.
The first time he sees Shilo that we know of, he starts screaming his head off in that musical number with the distinctive GRAAAAAAAAAAAAAAAAAAAAAAAAAAAVES!!!! I think his mind snapped under all the stress he's been living under, drug dealing and sleeping in a dumpster. The world is real, but the events in the movie were his brain's attempts to understand what was going on around him as he slowly died from the gas canisters the security men use. The last real face he sees before going under is that of an innocent looking teenage girl, but he can't quite get the face right. That ambiguity transforms into two people, the innocent naive maiden Shilo and the hypersexualised Amber Sweet with her constantly changing face.

The movie took place on the evening of Shilo's seventeenth birthday.
It would explain Shilo's Out-Of-Charachter rant that is "Seventeen".
 * ...This troper thought that is WAS her birthday.
 * It's never outright stated whether or not it is. There's no talk about a birthday anywhere.
 * I always thought she WAS seventeen, and she was just trying to get the point across to Nathan that she's not a little kid anymore.

The events of the Genetic Opera were all an elaborate suicide plan by Nathan.
When he found that he was assigned to repossess Mag's eyes, he finally snapped completely and decided that the only way to get out of killing his late wife's best friend was to die.

Amber Sweet has a thing for grave robber
She's not only insanely rich but also has a pipeline to Zydrate proper. Knowing those facts why does she trade sex for street Z? Simple to be closer to Graverobber
 * Her father may be controlling/cutting off her supply of money and of Z.

Nathan gave Shilo residual poison and her meds were doses of the antidote
Just as Baron Harkonnen slipped Thufir Hawat a residual poison that only he had the antidote for in order to ensure Hawat's loyalty to him, Nathan came up with a residual poison to use on Shilo so that its effects could be passed off as an illness and also to keep Shilo dependent on him. When Shilo spent too long a time out of the house, she would have died if she hadn't been brought back to be medicated with an antidote dose. If some of her "meds" were indeed poison, then she should have been feeling better after a long enough time without them. Even withdrawal symptoms shouldn't be triggering a collapse like the one Shilo had. Nathan thought this was a good idea because he figured he'd always be there to give her the antidote, but now he's dead and Shilo will also be in just a matter of time because Nathan can't give her the antidote anymore.

Mag knew all of this was going to happen
A side effect of her new eyes gave Mag the ability to see the future. The reason that Mag did nothing to stop her own death or gave any indication that she knew about Shilo was that Mag knew dying and allowing Nathan and Rotti to die would give Shilo her freedom.
 * And then there would be a reference to Greek mythology: the trope of the blind seer.