I severely disagree with your assessment of "Beast Machines": having lived with a war veteran with PTSD and having gone through a significant shake-up in my own life, I can tell you that the swift and radical departure of the Maximals' personalities is TOO radical and swift to be believable
I never said the Maximals manifested PTSD; although PTSD symptoms vary from person to person depending on the consequences. I said they reacted to their environment and adapted accordingly, and while I'd love to debate the nuances of the Maximal characterizations, perhaps I should take that discussion someplace else. I would like to mention, however, that the Maximals experience plenty of drama and development that is superfluous to the message
Beast Machines conveys.
That, too, I disagree with; by his own admission, the Vehicons were all defined in personality and action by one single trait: blind loyalty to Megatron and his goals. Yes, he tried to make them more "unique" by distinguishing to whom or what their loyalties lie - Thrust was loyal to Megatron, Tankorr was loyal to Megatron's goals but not Megatron himself, Strika and Obsidian was loyal to Cybertron, which they considered Megatron a part of, and Jetstorm...he was just a cackling psychopath who loved to cause pain (which is ironic, considering that's exactly what he accused the Predacons of being, and what he claimed to hate about them) - but in my mind, all it does is show just how much they're defined by that loyalty, and how much that loyalty revolves in some way to Megatron and his goals. Can we really call them "more flawed" and "less evil" if their only definining attribute and ambition revolves around their side of the parable? There's even a heated discussion on the TF board this guy's on over just how much free will they had, considering Megs would often delete any decisions they made that he didn't like. In my opinion, that makes them more animate drones for Megs, not unique, flawed villains, of themselves. They don't come off as "real" to me, in any sense, just dull puppets with arbitrary "quirky" personalities to hide the fact that they're dull puppets.
I'd agree with you in terms of the primary antagonist only. Megatron is 100% pure evil in Beast Machines, partaking in heinous activities that rank him among one of, if not arguably the most twisted Transformer(s) in the mythos. I'd have to disagree with regards to the other Vehicons however. How did Thrust's friendship with Jetstorm serve the parable? Why would drones with quirky personalities bother learning the meaning of friendship if they're all cookie-cutter metaphors? Obsidian and Strika weren't blindly loyal to anyone in particular, having to be reminded of the meaning of loyalty by Thrust. There was character development within the Vehicon ranks, they weren't only defined by servitude. Despite the fact that Megatron is my favorite character, I do feel bad for the Vehicon Generals; you're right, they didn't have a lot of control over their lives, and they were forced into fighting a war for a person that was only going to end up eating their sparks in the long run. They knew what was coming, and I'm certain they didn't enjoy the thought.
Megs' increasing problems to find an alternate way of bringing about his own goals for Predacon supremacy without resorting to tampering with the time stream resulted in his growing madness
What makes you think Megatron truly cared about his fellow Predacons? Sure, he spouted some rhetoric about it before trying to destroy Optimus Prime, but do you really believe that deep down, he cared about others beyond himself? And this brings me to my next point...
(did we ever find out how Megs decided organics and free will were useless?)
Megatron always hated free will. He always hated working with his troops. This is
clearly evident throughout
Beast Wars, where Megatron is shown to blatantly not care about his minions--even the loyal ones. He even experimented with drones in the form of Cyber Raptors; unfortunately he required a spark for the Transmetal II technology to fully function. Even with Dinobot II, Megatron expected his creation to obey him as a mindless puppet; and when he didn't, Megatron was furious.
As far as Megatron turning on both Predacon and Maximal alike through his "insane ambition", this was something predicted by the original Dinobot in "Maximal No More". So guess that makes sense after all, huh?
Finally, that leaves us with the hatred of organics. If you could provide me with quotes from Megatron lauding organics in Beast Wars, I'd be most appreciative. How are we to know Megatron enjoyed organics when the only "evidence" we have to support this lies with his delight concerning the power of his beast modes? Keyword there is power. That is something we know he appreciates, and given the nature of his situation on prehistoric Earth, a beast mode with power is quite a boon; yesss. After Megatron conquers Cybertron, he no longer requires a beast mode of course.
Alright, at this point, we've established that Megatron held no love of organics or organic life. But why did he
loathe organics? This is simple to answer. Organic life represents chaos and strife, while machine-like precision and efficiency exemplify order and control. Megatron is now the leader of a New World Order on Cybertron, and as a dictator seemingly obsessed with structure and the rule of law (his of course), guess which one he's going to side with? There's no indication that Megatron's ambition wouldn't eventually reach this zenith in
Beast Wars, so I don't see how anyone can claim this is character derailment. Megatron's diatribes concerning free will aren't developed out of any sort of dedication to an ideal; quite the contrary in fact, as he is clearly established as a hypocrite in the series--a point bolstered in Bob Skir's short story, "Singularity Ablyss". Megatron claims individuality is scandalous, yet refuses to relinquish his own when confronted with reintegration into the Allspark. His "single elegant machine" is an intricate characteristic of his own narcissism, megalomania, and extreme sense of personal individuality--ergo, all he really seeks is apotheosis. No different from his rantings in "Nemesis Part 2".
Is he a sympathetic villain? Hell no. He wasn't sympathetic in Beast Wars either though, so big deal. There's no grand dictum stating that antagonists need to be felt for, in either a parable or a character study. In
Beast Machine's case, a preset character like Megatron just so happened to serve the message; he wasn't crafted around it. Palpatine is very similar to Beast Era Megatron, and yet Star Wars isn't a parable. It should also be noted that Marv Wolfman's original story outlines didn't involve the symbolism and philosophy that Bob Skir imbued it with later on.