Because Destiny Says So: Orion Pax becoming Optimus? Megatron starting a global war that would destroy Cybertron? Yeah, the Covenant of Primus predicted it all.
Black Best Friend: Jazz for Optimus. Though he technically isn't black (being a robot), he fills the character role and takes some cues from his live-action movie incarnation, who spoke in slang and showed other black stereotypes.
But Now I Must Go: Inverted; Alpha Trion opts to stay behind on Cybertron, while the rest of the Autobots evacuate the planet.
Composite Character: Some of the Autobots and Decepticons appear to combine elements of their various portrayals throughout the years. For example, Optimus is a data clerk much like Dreamwave's War Within Optimus, while his preference for using swords in battle harken back to movie Optimus.
Continuity Snarl: Though intended to be a backstory for War For Cybertron and link it to Transformers Prime,Exodus contradicts both in several areas, and it even contradicts itself on a number of things. Alex Irvine explained at BotCon 2010 that differences between the novel and game were not due to miscommunications but, rather, resulted from deliberate choices as both products moved in slightly different directions; Hasbro was aware of and approved all of them.
Cyber Cyclops: Shockwave, as per tradition. Though you wouldn't know that from the book alone, as there isn't any reference to it.
Fight Clubbing: Megatron and a majority of the Decepticons were originally fighters in underground coliseums.
Flat Earth Atheist: Jazz doesn't believe in the Thirteen, seeing them only as abstract concepts to guide Cybertronians. To his credit, it's been a while since the Thirteen were around, and he most likely isn't alone in this belief.
Info Dump: The first chapter is immensely guilty of this. It takes information that could definitely be introduced later and throws it all into the intro. We don't need to know what the city looks like, when Orion Pax is sitting at a desk, and he's not even looking out a window — or even thinking about the city at all.
Mythology Gag: Before the Decepticons leave, Shockwave promises Megatron that Cybertron will remain "exactly as you left it." Megatron instructs him to be more progressive than that.
Debatably, and interestingly, Megatron seems to see Orion Pax/Optimus Prime this way.
Megatron also sees Shockwave this way, thinking that Shockwave can and would eventually turn on him.
Ultimate Universe: Like the rest of the new Aligned Continuity, the book combines elements of past incarnations of Transformers and combines them into one universe. For example, Primus and Unicron exist, but Primus used the All Spark to create the Cybertronians. At some point, the Quintessons invaded Cybertron, only to be fought back by Sentinel Prime.