Rotti Largo has a Myspace profile which suggests that there were smaller 'organ-financing' corporations before the main Geneco was set up - specifically, it mentions Rotti training in his father's business, Geneco of Milan. So...Why not have the Union set up to deal with the organ failures in 2030? Eventually, as Geneco takes more of a public stance towards ending the organ crisis, it begins to buy out other similar businesses, to eliminate competition. After it becomes the sole provider of these services, we reach 2056, when Geneco effectively owns what seems to be the last functioning city, and all the other Repo Men (possibly hired from the companies it bought out - we see a few of these in the comic-style opening sequence) are slowly phased out in favour of a single Repo Man.
- There are still multiple Repo Men in the world of the Genetic Opera, though the musical focuses on only one. They can be seen during Night Surgeon and showed up in deleted scenes. The theory still holds up.
- Beth survives and becomes the lead heroine.
- Jake becomes an Anti-Hero/Anti-Villain. He becomes determine to capture Beth, because he blames her for what happened to Remy.
- Carol and her son get caught in the middle.
- In a bit of irony and Karma Houdini, Jake ends up getting a transplant (perhaps thanks to Beth). He ends up in a similar predicament as Remy. Yet, he follows his belief so deeply that he's pretty much in denial of the situation. Which leads to a Villainous Breakdown in the climax, and commits suicide rather than go against his belief.
- You forgot one detail: Due to Jake finding the underground hospital with tons of spare replacement parts (presumably from people who died that were salvaged for those who need spares that can't afford the cost), he tells the tech that has Remy hooked up "All of that should cover the cost" after the tech mentions the cost of the unit. Seeing that was just one room, and that Jake has basically lead a whole team to the place, the repo payday for recovering that many replacements more than likely lead to a major payday to cover the cost of Remy's dream state.