The overall mood is  much darker than before and has given a real Cyberpunk feel to Transformers. The action is faster, the explosions are bigger... the 3D models look better (just compare their beast modes to how they looked in season one of Beast Wars!) and there are shadows everywhere!!

Beast Machines elevates the Transformers to a whole new level of excitement.
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Technorganicism
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This concept has garnered a lot of negative feedback from fans. Many were outraged that the Transformers could allow themselves to be merged with organic matter. Many even found the suggestion that Cybertron was once an organic planet to be sheer heracy. However, the Marvel Comics did state that Primus himself created Cybertron from an asteroid - one that could have supported organic life before his intervention.
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The Philosophy...
(familiarity with Aristotle's philosophy of Cicero would be useful before reading on...)
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Like the Chinese philosophy of Daoism and Aristotle's notion Phronesis ("human reasoning" - which was part of his philosophy of Cicero), the Oracle's notion of Technorganicism advocates that harmony is found within the balance of two extremes. In Daoism, it was the concept of Yin (dark) and Yang (light). Aristotle stated that there are true virtues are those which lie midway between what he calls Cardinal Virtues. For example, stupidity and cowardice are cardinal virtues and courage is the true virtue that lies between them. Of course, being the tutor to Alexander the Great allowed this philosophy to spread throughout the world during Alexander's conquests. This all becomes evident in season two of Beast Machines.

We see Optimus Primal and Megatron representing the two Cardinal Virtues of Technorganicism (although Optimus Primal changes his views drastically by season two). In season one, Optimus Primal represented the Organic Cardinal Virtue. Megatron represents the Technological Cardinal Virtue. Technorganicism, the balance between the two Cardinal Virtues, is the true virtue that lies between. So really, during season one of Beast Machines, neither the Maximals nor the Vehicons were righteous (although both believed each other to be so).

I think it was really interesting to see the lines between 'good' and 'evil' becoming so blurred. It has heightened the Transformers saga to a whole new elevation never seen before!
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The Matrix
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Let's have a look at the different incarnations of the Matrix:
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1. The Autobot Matrix of Leadership.
In the G1 TV series, the "Autobot Matrix of Leadership" and was first seen in Transformers the Movie where Hot Rod used it to destroy the planet eating monster, Unicron. In the episode "Five Faces of Darkness," it was revealed that the Matrix was the font of all knowledge and contained all the wisdom of past Autobot leaders. It could also be used to interface with Vector Sigma, the Super computer who created life on Cybertron.
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2. The Creation Matrix.
In the Marvel Comics, it was referred to as the "Creation Matrix" and was tied in with the very genesis of the Transformers, as told in the comics. The Matrix itself was a part of the Transformer god, Primus'  life essence. It was a sacred object that could destroy Primus' nemesis, Unicron. The Creation Matrix was destroyed in issue #75 of the US comics, when Optimus Prime plunged himself into Unicron, sacrificing himself.
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3. The All-Spark Matrix.
Throughout Beast Wars, the Transformers made several references to the Matrix, but mainly as another plane of existence where deceased Sparks would go. This was very strongly demonstrated in the season two episode, "Code of Hero," with the death of the Maximal, Dinobot. Even earlier in the same season, Rhinox delved into the Matrix to find Optimus Primal's Spark. He referred to it as the place where 'All Are One,' which is a direct quote from Optimus Prime. This is what some have come to call the "All-Spark" Matrix (which is how the Oracle describes it), to differentiate it. The true nature of the All-Spark Matrix was finally explained in Beast Machines.
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4. "Maximal Matrix of Leadership."
Even in Beast Wars, Maximal leaders Optimus Primal, Lio Convoy and Big Convoy all carry their own personal Matrices, which was a different concept from the All Spark Matrix. Galvatron carried an orb known as the Galvamatrix, which was bestowed by Unicron (since Galvatron was nothing more than Unicron's pawn).
Although the origins of these Maximal Matrices were never conclusively explained, it would be reasonable to presume that they were created by the Transformer god, Vector Sigma who was portrayed as the archnemesis of Unicron in Beast Wars Neo (obviously a substitute for Primus, since Primus was never in the Japanese continuity).
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The Oracle (most of this is personal speculation)
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What is the Oracle? This is one of the greatest mysteries of Beast Machines. The Oracle is a combination of the All-Spark Matrix and Vector Sigma (as seen in "The Key"). According to legend, the Oracle foretold the coming of the first Transformers to Cybertron. This would suggest that in the beginning, there was the Oracle. Then, for some reason, the Oracle divided into two, with the two halves becoming the All-Spark Matrix and Vector Sigma. The fact that the Oracle existed before the creation of Cybertron and the Transformers would explain Vector Sigma's statement, "Before Cybertron was, I was" in the G1 episode, "The Key to Vector Sigma" (where the Stunticons and Aerialbots were created). By Beast Wars, Vector Sigma had reverted back to its more divine origins. In Beast Wars Neo, Unicron possessed Vector Sigma, and tried to transform Cybertron into his new body. He was foiled by the combined might of Lio Convoy and Big Convoy's individual Matrices. I speculate that some time after that, Vector Sigma decided to reunite itself with the All-Spark Matrix, becoming the Oracle once more. This was probably done for a variety of reasons. One of them may be to protect itself from Unicron, should he ever try to possess Cybertron again (since the Oracle has the power to disappear and reappear at will, something Vector Sigma could never do). But most likely it was done in preparation for Cybertron's next phase of evolution to Technorganicism.