So, Chris, if you're reading this, great; I have an idea for the BCC Conspiracy Show that I would like to tell you! (derp)
Here it is - the entirity of Mixels is a ploy by Makuta Teridax to make the Matoran believe that the Toa are the worst thing ever, and that Teridax is the best guy ever and should totally rule over them. Here, let me show you what I mean (or rather, Kadihi; he's going to be the only one taking this seriously. I know I'm not taking myself seriously. :P),,,
The Mixels are (obviously) supposed to represent the Toa. The large amount of colors and elemental powers, not to mention the ability to combine into larger beings made of three components (Maxes and some Mixes), just kinda makes it "obvious". However, in the Mixels TV Series, the Mixels have been shown to be incredibly greedy to the point of violence, backstab their own kind without any sign of regret or guilt, cause massive amounts of destruction, act like complete animals, be dumb enough to the point where they're duped by a shadow puppet, and overall be generally despicable. Potrayed in a positive light, they are not.
The Nixels are obviously supposed to represent the Makuta, or possibly their minions (Rahkshi, Visorak, ETC). While the Nixels have been shown to be dumb at times, they have also been shown to be clever, such as knocking away cubits so that the Mixels can't use them, attaching themselves to a cave entrance because they knew the Mixels were there, even though the trick in that example usually works, and they have also been proven to be highly versatile. The one Nixel used to represent Teridax is Major Nixel; King Nixel is shown to be a tyrant and a coward, two things Teridax wouldn't want to associate with himself; King Nixel most likely is supposed to represent Miserix.
See? IT IS SO OBVIOUS! (not really, but this will work very well for the average konspiracy. (derp))