Why does Megatron hate organics when he was previously organic himself? Simple. It was just a means to an end. All he really wants is godhood, and being partly organic prevents him from becoming one with the mechanical planet that is Cybertron.
On top of that, Megatron was already unhinged by the end of Beast Wars. It’s entirely possible that by the time he fell out of transwarp and landed on Cybertron, he had gone completely insane.
In the previous series, Megatron was ultimately revealed to be the Cybertronian Antichrist. In this series, he takes over the world for a time and is defeated by being cast into a pit as the world is reborn as a paradise.
Rhinox Starscreaming once he surfaces from Tankor. It’s what he did the last time Megatron turned him evil.
Megatron's motivation makes a lot more sense if one considers the events of Beast Wars. Look at how much his minions betray him - only two remain loyal, and one of those is just barely competent. Is it any wonder he would come to consider free will itself to be the problem?
Thrust being Waspinator makes perfect sense when you look at the flashback he has. Why else would the Maximals not be happy if he's one of them.
When they fight, Optimus is able to fair better against Megatron's Dragon form than he did in his Optimal form (which is later shown to be stronger than his current form). Given Megatron mutilated himself trying to purge himself of his organic aspects, it's likely he weakened himself in the process.
