(tl;dr at end)
Ah, Repo! the Genetic Opera, a musical that will always have a special place in my heart. An original, quirky and instant cult class, something not seen since the Rocky Horror Picture show. I love it, simple.
So many questions unanswered in such an in-depth and complex dynamic universe.
After thinking about it a tiny bit, one of the biggest question for someone who is as big of a hypochondriac as myself is ...how clean are those organs once reposed?
This brought on my latest fan theory about the series: GeneCo created the disease that wiped out most of the human race, then proceeded to cure most disease and infection...to increase their profits.
Throughout the entire movie, we are riddled with scenes of Nathan cutting open his victims and taking their organs for re-use by GeneCo. Look at the gore throughout the movie, and then look at how exposed to blood and fluids several of the characters are. None of them seem particularly worried about it, and while the world of Repo! is desensitized to violence, what about all the disease that lurks in humanity, even in the 21st century?
At some point in the Repo! universe, a lot of people died, and then GeneCo came along and offered the solution: genetic perfection. From what we've seen of GeneCo, it's clear the company was set up, and pardon the conspiracy theorist in me, but it's always odd when something hits such a large population with one cure brought forth by a private company.
Now I know the premise is that GeneCo offers organ financing and all they do is replace old organs with new, but evidence suggests they do much more:
In the Limo, Rotti states he is making the cure to all blood diseases, which Shilo takes as credible.
The Grave Robber even sings about genetic perfection, in the very first song.
My theory is simple: GeneCo created the disease that killed those millions, then retracted it. How? Zydrate. I assume that in the Repo! universe, all of Rotti's patients were given Zydrate; as a common delivery method to the sick, it destroyed the disease that killed the old organs.
The people who didn't get sick? Either GeneCo employees or simply unaffected by the disease. We see in the intro sequence that the body movers were wearing gas masks, which would give logical reasoning to the disease being air born. That's not really important though. No where in the history of the main characters do we see them affected by the disease - all of them are either GeneCo employees, family of Rotti or born after the disease.
So GeneCo has their permission to finance organs in place, but there's always that problem of contamination, so that would ruin the reposed organs, eh? Not if GeneCo cured most disease to save their stock - the characters in Repo! have no fear of being sprayed with blood, we don't see Nathan wash down his suit with anything more than water - which is an awful cleanser - and sexual attitudes seem to be pretty free with no concern to HIV or Aids.
We even see the Grave Robber take Zydrate from the freaking dead, and no one has a problem with this - that must be one sanitized world.
None of the characters in Repo! are ill (except for Rotti), and why is Rotti ill? Because he never had any treatment - not a single bit. Happiness is not a warm scalpel is his direct quote. He never had treatment, never took any measures to use his own methods due to knowing what it would cost his pride.
tl;dr: GeneCo created the deadly disease, cured it through something in Zydrate, cured other disease to be able to use organs over and over again