"The Quintessons story says that the Autobots and Decepticons were manufacted together and lived together all along, but in the Season 2 episode, when the Aerialbots go back in time, Orion Pax says of the Decepticons, "They're a new kind of robot that can fly!", which seems to imply that they were not around in the beginning. "

When cartoon series have contradicting plot points, when I have to consider what is "canon", I go by what came first, not which theory I like the most. In Season 2, "The Key to Vector Sigma" parts 1 & 2, it is expressly stated that VECTOR SIGMA created the Transformers (Megatron says to him, "I am one of your own creations"), and possibly Cybertron, too. (Evidenced by his line, "Before Cybetron was...I was!" and the fact that the key to Vector Sigma could turn a normal planet until a Cybertron-like planet.) The Vector Sigma theory came first, so that's what I go by. As for Orion's line about the Decepticons being "a new kind of robot"...Again, going by what came first, there is plenty of evidence the Decepticons were there all along, but they weren't always enemies of the Autobots. Remember in the episode where they first meet Skyfire, Starscream was a scientist before he became a warrior, and Megatron mentions "A final falling-out with the Autobots". Maybe Orion lived in a part of Cybertron where the Decepticons had never been to and he had never heard of them until now (Cybertron is an entire planet, it's not unlikely), so that's why he thought they were new.

With that said, I think Season 3 sucks for the most part, but I do like "Call of the Primitives", "Grimlock's New Brain", and "The Return of Optimus Prime" (except for the ridiculously cheesy way that one ends and the fact that I don't understand why Prime's lifeless body is piloting a ship into the sun in the beginning, but oh well...)