* Micromasters were explained as Cybertronians who had downsized to become more energy efficient. In Beast Wars the Maximals and Predacons continued to be Micromaster-sized and BW Megatron once referred to the Autobots as "archaic Energon guzzlers."
* In the Armada cartoon continuity the Mini-Cons were indeed a separate foreign species introduced to Cybertron by their creator Unicron.
* In the Armada comics Cybertron was a caste society and the Mini-Cons were a lowly underclass that nobody paid much attention to. The Decepticons captured these Mini-Cons and surgically modified them to power link and boost their host's power.
* In the IDW comics the original Mini-Cons were descendant from the colonists who followed Micronus Prime aboard the Titan Prion. The Black Block Consortia effectively committed genocide against these Mini-Cons, exterminating almost all of them. The only known survivor, Nickel, fled and joined the Decepticon Justice Division.
* The IDW comics also introduced a non-Cybertronian species known as Stentarians; a race of transforming and combining robots. They have been waging a long drawn civil war between the heroic Terradores and evil Ammonites. Hasbro released one set of Ammonites which they marketed as the Mini-Con Assault Team. Shockwave managed to gain control of the Ammonites and commanded all seventy billion of them to descend upon Cybertron (so much so that they blotted out the stars in the sky), keeping the Cybertronians occupied as Shockwave ascended to godhood in order to collapse time-space into a singularity. As you do.
* In the Aligned Continuity the Mini-Cons shared a similar origin with IDW (re: Micronus Prime). The Aligned Mini-Cons are very diverse ranging from the Arms Microns to Deployers to mass-produced drones like Fixit.
* Generation 1 (CHUG retcon; USA): Mini-Cons were created by the Last Autobot to cleanse Cybertron of Mutants and Demons. Which is actually incredibly horrific when you remember that the Mutants and Demons were the indigenous species of Cybertron before Primus came along and reshaped it as Cybertron and populated it with Transformers!Yeah. The Autobots and their Mini-Cons committed genocide against Cybertron's indigenous race!
I get that the Demons and Mutants are incredibly hostile and savage (practically Morlocks)... but still. How was Optimus Prime cool with this??
* Generation 1 (CHUG retcon; Japan): Mini-Cons are a sub-faction of Micromasters who have become able to power up their hosts by connecting with them as weapons etc.