Shades of Grey/WMG

The Riff Raff are the real future humans. Homo Coloribus are the result of extraterrestrial and human crossbreeding.

 * Point 1: The Riff Raff seem to see at least more than one color and aren't affested by artificial colors (or at least it seems that ), like us.
 * RiffRaff can, there's a mention of some captives that did (most captives do, it's implied). It might have been a lie, like most things concerning  , but it makes just as much sense that it's technically true that they caught it.
 * Point 2: The Riff Raff refer to themselves as "The Digenous" as in indigenous, which means something along the lines of "the original inhabitants." If they (or their ancestors) considere(d) Homo Coloribus invaders, this name makes perfect sense.
 * Alternatively, by crazy etymology, "The Digineous" could mean the opposite to indigenous, and they're the outsiders.
 * Point 3: The whole "invaders" angle also gives them good reason to hate Homo Coloribus the way they do.
 * Do they really hate Homo Coloribus? The only ones we actually meet seem not to go much beyond dislike, and most of the what we hear about the Riff Raff is probably just propaganda.
 * Jane seems to think so. And it's not like they don't have plenty of good reasons to, the Collective hoards all the good land and Previous artifacts they can get their hands on, forcing the RiffRaff to scrape a meager existence in the wilds (which are infested with megafauna and yateveos, the latter of which was specifically created by the Collective to kill RiffRaff!)
 * Point 4: The author even hints at in in this article. He says in the section "Colour Vision Deficiencies" that the fact that everyone can only see one color is near impossible in modern humans, leading one to "consider that Eddie and his kind are not like us at all." The colorblindness could be the result of a genetic defect caused by extraterrestrial and human DNA combining.

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.
 * Alternatively, that is where Ultra-violets come from.
 * Jossed. Ultraviolets are just very highly-perceptive Purples.

Additionally, the offspring of people of complementary colors are
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 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.

The Shades of Grey universe is the future Pokémon universe
You read it here first! Cities in this universe have similar or identical names to those in the first-generation 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 Computer
You 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 Office
Jane mentions late in the book, that  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
 * But that's kind of the point - the society is so messed up that even a reasonably decent man will do something that unpleasant. Pimping out your own children is endemic.

The Colourman is
As shown in the end,  You heard it here first!
 * This was something I thought as well, going through the book.

The main characters are all robots, the Riff Raff are the remaining real humans
The 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.
 * That seems very unlikely, given that they can reproduce and everything. Artificial Humans, perhaps, but Ridiculously-Human Robots seem unlikely, especially given the fact that the Bestiary on the website does show some genuinely robotic 'animals' such as the Asimov Horse.

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 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.