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 than 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.
Jetfire is an elite pilot in the Transformers saga. Thus, his alternate mode of a SR-71 Blackbird is a fitting choice: it's an outdated aircraft, but considered one of the fastest and highest-flying planes to have ever existed.
Soundwave as a satellite fits his role as a Decepticon spy. He can stay in space and keep surveillance on events happening on Earth, and he can deploy his minion Ravage to carry out his orders.
The Barrage Cannon Optimus shot Megatron with is described in supplemental materials as firing shells with plutonium tipped warheads with explosive force equal to 3000 lbs of TNT. The reason it only knocked Megatron out a window is that point-blank is too dangerously short for the warhead to arm. If Megatron had been hit at a considerable distance it would been a different outcome.
The Fallen's rather quick death at the hands of Optimus Primes' Curb-Stomp Battle initially seems rather off-putting and has even been criticized as being anti-climatic, given that, up until the end, The Fallen's malevolence and threat has been slowly built up over the course of the story. However Optimus' rather swift dealing with The Fallen can perhaps be explained from a few factors:
First and foremost, it was mentioned earlier by Jetfire that, "Only a Prime can defeat The Fallen," so therefore, Optimus already had an advantage over The Fallen by being The Fallen's equal in strength and power, since The Fallen was originally a Prime himself.
Second, The Fallen has been hiding away out of fear of The Last of The Primes still being out there in The Universe for what was clearly thousands of years, all the while, Optimus and the rest of The Autobots have been constantly gaining further experience and battle and always taking the time to hone and maintain their natural fighting skills. As proven when he finally reveals himself on Earth, The Fallen is clearly relying far more on his secondary powers of Teleportation and Telekinesis rather than his own physical abilities to deal with any opponents. Afterwards, when he is subdued and forced into an proper fight with Optimus, The Fallen is quickly overpowered and barely manages to land an attack on Optimus at all, with Megatron offering support being a major reason as for why he (The Fallen) lasted as long as he did!
Third and finally, in connection with the above statement, it also didn't help The Fallen's case that Optimus also attacked The Fallen and Megatron right after he had just received additional parts from Jetfire, which only made him even stronger than before (being capable of sending Megatron flying through the ruin walls with a blast from his new jet engine pieces), hence both The Fallen and Megatron were completely at Optimus' mercy this time.
One of the tie-in comics reveals Demolishor purposely hides so that large forces like NEST can come in and he can kill them. Which, as TFWiki.net pointed out, makes the opening Shanghai scene more sinister……
