For Wild Mass Guessing about the rest of the franchise, see Transformers.
Waspinator has a crush on BlackarachniaNotice how in Beast Machines, Thrust (who has Waspinator's spark) reluctant to hurt Blackarachnia, and even saves her life a few times. As he regains his memory, he becomes more willing to help her, and there's a definite romantic undertone to his flashbacks. Hence, he had a thing for the sexy spider.
In Beast Machines, the virus did affect the Transmetals, just to a lesser extentResulting in their drastic personality shifts for the worse (removing Rattrap's heart of gold leaving just a coward, turning Optimus into a fanatic follower rather than a compassionate leader). Cheetor and Blackarachnia got the least affected, being Transmetal 2s, but Blackarachnia, being more emotionally vulnerable, showed more change, while Cheetor, having no attachments for the virus to enhance into a critical weakness, managed to overcome it and become a badass, although the virus did wipe out what little innocence he had left.
Scars over the eyes were in style on Cybertron when Megatron took over.Having been on Cybertron for a while before taking over, he picked up a few new fashion trends. Once such trend was a scar over the eye and Megatron liked it so much he decided to keep it after taking over Cybertron. He even gives his new Optimal Megatron body the same scar out of habit for that fashion trend that no longer exists in a world without people to create fashion.
The Story would have gone completely differently had Dinobot II gone with the others back to Cybertron.This Dinobot, being a transmetal would survive the virus with the others, and been reformatted. He would also be able to transform more easily than the others due to his expertise and slightly more spritual nature. He would have been able to use his tactical skills to improve their chances of victory against the Vehicons and stop having to hide in the catacombs all the time. He would also call out Optimus on his rather aloof behavior, and convince Obsidian and Strika to assist them against Megatron. Finally, he would prevent Rattraps Wangst due to their ahem, special relationship. In short, Dinobot would have made a good Team Dad to prevent all the others' Character Derailment.
Rhinox didn't side with the Maximals because he hated his old beast mode.Of the original four maximals, Rhinox was the only one that never got a transmetal upgrade. When shielding from energon radiation was no longer necessary thanks to the Vok, Rhinox's beast mode became useless while the transmetal maximals could fly/drive in their beast mode. Rhinox only used his beast mode twice in season two and never used it at all during season 3, which shows that even in Beast Wars Rhinox believed an organic beast mode was obsolete. As Tankor he feared that if Optimus succeeded in reformatting Cybertron Rhinox would be given an equally useless beast mode.
Everyone on Cybertron dies within a month after the end of the series.According to certain comic universes, Primus made Cybertron out of an already inhabited planet. The original inhabitants were forced deep below the surface, but the few times they made it out from underground they slaughtered every Transformer they came across with very little difficulty. It's only that metal shell on the planet that's keeping them safely separated from the Transformers and that metal shell juuust got taken down...
Megatron was possessed by Starscream's spark the whole time.This makes a frightening amount of sense. It would explain Megatron's seemingly random personality change between the two shows and how "his" spark later goes around taking over other bodies on its own. The only thing it doesn't account for is the sudden loss of ham, as Starscream was always as much or more of a Large Ham than Megs, but he did have millions of years of floating around space to turn emo.
Megatron as they knew him was actually G1 Megatron.Remember how crazy Megatron became after carrying his namesake's Spark around towards the end of Beast Wars? That was because G1 Megatron was slowly overwriting BW Megatron's mind, slowly but certainly metastasizing inside his unwitting vehicle and writing a shell program around his mind, which lingered even after the Spark was removed. G1 Megatron's Spark was then sanitized by the Maximals so he could never take advantage of the knowledge stolen from his future namesake, but the shell program remained inside BW Megatron. Learning that humankind was responsible for the Decepticons' losing the Great War turned this new Megatron violently anti-organic, and the sheer trauma of the experience coupled with the knowledge that the free will of the Autobots would shatter his grand visions for the future drove him completely insane, prompting him to wage war on the "curses" of individuality and free will. Becoming a Physical God was either always his master plan, or a product of his newfound intellect. His agenda even reached behind the scenes of Beast Machines, freeing G1 Megatron's actual spark from whatever prison the Maximal Elders kept it in and constructing the Big Floating Head to house it (the Spark was mutated from the touch of Unicron, hence its strange properties seen in Season 2). But Optimus Primal threw a spanner in the works and destroyed BM Megatron once and for all in "Fallout," as well as shunting G1 Megatron's Spark into an organic form.