But the show does explain it. If you follow the Oracle (and Primal's) statements, it can be surmised that the Oracle wants to restore the organic to Cybertron, because apparently it feels that the pendulum has swung too far in the direction of the technological. "Seek the balance" it tells Primal at one point, implying that the current state of the planet is not 'balanced'. As Primal later says, when he finally wakes up and abandons the fanatacism he had during the first season, the Oracle never intended organic to replace the technological, but that both co-exist.
Yes, if there's one thing I do appreciate about the show, it's the message that extremism is the true failing of any philosophy. Which is, of course, surprisingly layered for what's technically a kids' show.
The problem is that it's never at any point explained why a balance between technology and nature is needed at all, much less it being an advantage. Cybertron did fine without any major natural influence for the past several million years, what does it need this for now? The angle that it was originally a planet populated with natural life does intrigue, since whatever the Oracle is or is influenced by, it must be separate from the Transformers and their established origins. Brings to mind the surprisingly similar assistant to Primacron from the oddball G1 episode Call of the Primitives.
I've also been fond of the theory that the organic aspect will result in shorter life-spans, and thus more knowledge being brought back to the Allspark. The sort of seemingly indifferent action likely to be a primary goal of a deity, especially one that created such long-lived children..
The motivation that's unclear is Megatron's. His hatred for organics is a character shift that comes out of left field, given that he never expressed any such feelings during the Beast Wars. Some support for his newfound fanatical hatred would have been helpful. If it was an effect of having G1 Megatron's spark in contact with his own for so long, then a line of dialogue to explain that would have been sufficient. But it's never explained, and the audience is just left to accept his motivation as a matter of fact.
Again with the theory - with Megs falling off the shuttle in transwarp, it's likely that his organic components could have caused him extreme pain with their exposure to the vacuum of space. Again something and could and should have been shown in the show with a single scene, but an interesting thought all the same.