Repo Men/WMG

Mostly everything is going to return to normal

First off, Jake hints that he was going to take care of Beth soon. Remeber how Remy notes that she has nearly all her organs replaced by Artiforgs save for her heart (this is just how I interpreted the line). Well, she won't be needing that if most of her Artiforgs are vital, and it was not established wither or not Remy and Beth have the same blood type or not. So what might happen is an organ transplant. Second off, if that whack on the head put Remy in a Convenient Coma, then it might as well give him Easy Amnesia, causing him to forget everything from the time the defib nearly killed him to the point where he got whacked in the head. Including his remorse for the people with Artiforgs. Again, mostly everything because there is still that whole Carol issue to fix.

Repo Men and Repo! The Genetic Opera are set in the same universe.

Just bear with me for a second.

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.

What the sequel will be about...

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.

Jake, subconsciously, tries to get back at Remy.

When they were kids, Jake was a bully until Remy stood up to him. Since then, Jake was seen as a joke, which he resented Remy for, but not out loud.