While Lelouch and Suzaku serve as parallels to Optimus and Megatron, their distinctions allow insight into why one relationship works while the other doesn't.
While Lelouch's methods in obtaining victory are all too much like Megatron, his goal in making a better world for his sister is completely genuine; a little self-centered but a far more noble goal than Megatron's ambitions. Optimus's former incarnation's mission was to better understand individuals and find peaceful resolutions so helping Lelouch is just him carrying out that goal.
While Megatron and Suzaku both climb the ranks, their feelings about it are way too different for any of them to connect. Megatron takes pride in his actions, good and bad, and if he did something wrong, he would push forward to correct the problem. Suzaku on the other hand, when faced with adversity, runs away.
There's also the matter of how Suzaku never takes responsibility; something Megatron knew far too well from a certain corrupt Autobot politician.
Another reason why Lelouch quickly develops respect (and later affection) for Optimus Prime is perhaps not just his natural charisma, but his empathy. As stated by C.C., the only one she knows whose compassion can rival Nunnally's is Optimus himself; Lelouch probably can't help but notice the similar quality between the two, and seeing as he loves his little sister with all his heart, he unconsciously grows to be a little receptive of someone who reminds him of her, despite his justified difficulty with trusting others.
Continuing from this, Optimus Prime is a being whose ideals stand in direct contrast to those of Charles zi Britannia and Megatron: both preach that strength is what matters, and if you are weak, then you are only a pawn (though Charles is putting on an act). Optimus has great power as a fighter and leader, but he fights for peace and freedom for all people. This definitely makes him the sort of person Lelouch would wish he had as a father: a powerful warrior with a noble soul who uses his abilities to protect others, not dominate them.
Why would Starscream be so submissive to Megatron even though the events of "Rock Bottom" never happened? Remember, the events of "Transformers: Fall of Cybertron" actually happened in this continuity, and fairly recently at that; meaning Starscream had already staged his coup, began his time as a rogue Decepticon, freed Grimlock and getting the snot beat out of by mentioned Dinobot. Most likely the two latter events had impressed Megatron to give Starscream another chance, not before dishing his usual beatdowns on him to ensure Screamer gets the point.
If Unicron is connected to Geass, why can't Geass bearers affect Cybertronian yet? That's because Cybertronians have lived far longer and are able to adapt to counter the Geass for a while.
Furthermore, if Unicron is connected to Geass, then it makes sense. As the author has confirmed that Unicron is the core of the Earth like he was in Transformers: Prime, then that means everything and everyone on Earth came from him, including Geass.
The Decepticons' disunity and contempt with the Holy Britannian Empire goes deeper than just seeing humans as an inferior species — Britannia enforces a Fantastic Caste System that is in several ways reminiscent of the one that had been implemented on Cybertron prior to Megatronus's uprising, which many of the earliest Decepticons had originally been oppressed by.
Normally Geass sigils are colored red which is the same color to most of the Decepticons' eyes. However thanks to C.C. and the other Thirteen Primes, Optimus's Geass sigil is white. This not only shows that he's first and foremost an Autobot but also telling that he's The Thirteenth Prime.
