Skids and Mudflap actually picked a pretty good disguise, from a Cybertronian point of view. Firstly, they were rolling around in Shanghai, where you wouldn't see too many classy cars. And secondly, Refuge in Audacity - nobody would expect a robot who could choose any car they wanted as their alt, to pick something that beat-up and stupid.
The Fallen's motivation and methods are similar enough to Apophis even without the whole "Will rise again" mantra, which is very appropriate since the climax takes place in Egypt, where historically the people regularly prayed that Apophis would not win. It takes an almost literal Deus ex Machina for The Fallen to lose. The transformers themselves are similar to the Netjeru, in that they very capable of being killed and may fall apart with age, but can also be restored to youth, even brought back to life(through energon rather than magic) and can become stronger by taking on each other's aspects. They are also aliens, which ties to the common Ancient Astronauts "theory" regarding the gods of Kemet, but rather the pyramids being the work of alien tools they were instead hiding the real alien technology, and it's really modern society that owes it's wonders to alien intervention.