The Riff Raff are the real future humans. Homo Coloribus are the result of extraterrestrial and human crossbreeding.
The Something That Happened was an alien invasion.You heard it here first.
The offspring of people of complementing colors are no longer colorblind.This is why people of complementing colors are forbidden to have children: Once someone sees all color naturally the Head Office has no control over them.
Additionally, the offspring of people of complementary colors are immune to the Mildew.We know that people who see colors naturally are unaffected by the artificial colors that affect other people (natural Greens can't go to the Green Room when they're struck by the Mildew (as mentioned in the chapter 'One Eyebrow')). We also know that The Mildew is a color, a "greeny-red." So any children of complementary colors would not only be able to see all the colors, they also would naturally see green and red, and thus they would be immune. Pokémon games (Vermillion, Cerulean, Cinnabar), and the wilderness around them is populated with strange animals, all of which have (apparently) naturally-occurring barcodes somewhere on their bodies, taxa numbers that once upon a time would have been used to log them into the Pokédex.
It's all an experiment run by Friend ComputerYou want a reason? Well, only being able to see the colour of your Clearance Level would stop people going into areas higher than their clearance. Now please report to the nearest Termination Booth for questioning Friend Computer's reasoning.
Holden Russett is secretly working for Head OfficeJane mentions late in the book, that swatchmen are generally lackeys for Head Office, infecting unruly citizens with the Mildew. Although she believes that Holden is not an evil man, it's entirely possible that he is edging Eddie on, pushing him forth into situations where he will either be captured by agents of Head Office or inadvertently reveal pertinent information to them about the resistance. After all, it takes a pretty shitty dad to set up his own son to be raped.
The Colourman is Eddie's fatherAs shown in the end, Eddie's dad is not his dad at all. So, the only person introduced to be high enough on the red is the Colourman, and he says that he is somewhat 'related' to Eddie. You heard it here first!
The main characters are all robots, the Riff Raff are the remaining real humansThe Something That Happened was the robot revolution. The robots all had a massive sense of inferiority over the fact that they were not real creatures, Munsell's Epiphany was that if the robots did not know they were robots then they were free to live happy lives. The point of the Leap Backs is to bring science so low that no-one can even comprehend the idea of what a robot is. This is how everyone has a bar code and how they can have programmed responses to colours and sounds.
The original humans invented space travel and left Earth. The people who were left behind have been subject to intense genetic alteration and/or testing.Jane specifically mentions the "lights on the dark part of the crescent moon," which apparently look like stars. These seem a lot like moon bases. Taken into account with the other lights that streak across the sky, some of which are probably meteorites, some of which might be satellites, and others of which might be space stations, you get what a spacefaring civilization might look like to an earthbound human...ish. Perhaps the Fallen Man was meant to be looking in on the remnants to see how they're doing when his lander failed or something.
Homo Coloribus and indeed the entire Collective are a huge experiment to test something unknown or a bizarre future theme park, perhaps both.It would explain all the limitations on space and population that the citizens have to deal with, as well as the strict adherence to the seemingly arbitrary Rules. The barcodes on everything can be explained as the people running the show wanting to keep track of everything in their mock environment. The line about giant swans flying so high they sometimes don't seem like swans suggests that they are planes doing fly-overs of the environment and the Fallen man who seems to be a pilot who didn't eject safely supports this. Then of course the bizarre limits on a Collective citizen's vision, their differing appearance to modern humans and their heavy lifelong condition suggest heavy genetic alteration. This doesn't really explain the presence of Riff Raff though.