Top 10 Burning Questions from Transformers 2 (Updated)

This post pretty much assumes you have seen the movie, so spoilers within.

If you’re a fan of science fiction and comics, part of the fun is coming up with explanations (sometime elaborate ones) to explain inconsistencies in continuity. As my review of the movie indicated, Transformers: Revenge of the Fallen has story holes large enough for Optimus Prime to drive through. From Yahoo! Movies here are top ten questions (really more then that) about Transformers: Revenge of the Fallen, many of which will probably be beyond the ability to retcon. Thanks to aunit2011 for the link.

1. In "Transformers," there was this giant battle in the middle of downtown Los Angeles -- excuse me, Mission City -- that was witnessed by thousands of people at the very least. But somehow the government was able to cover up the whole thing, and now the existence of alien robots is just an internet rumor? How did they do it? Pay off everyone who was there and quickly fix millions of dollars in damage? Also, didn't Keller (Jon Voight) go on TV and tell everyone we were being attacked by "a technological civilization far superior to our own"? How did they spin that?
If remember, the novel said Mendelson Robotics is blamed as part of a failed test of new weaponary. Also at the end of the first movie Keller even indicated it was explained as a failed training exercise.

2. There are two pieces of the Allspark cube left: the military has one under lock and key, and Sam discovers another. The Decepticons steal one and bring Megatron back to life. But when Sam (Shia LaBeouf) wants to bring back Optimus, he has to find the Matrix of Leadership on the other side of the globe. Why not use the other piece? Mikaela (Megan Fox) has it in her backpack the whole time. It brought his kitchen appliances to life, why can't it do the same for Optimus?
Mikaela's shard was used on Jetfire

3. Speaking of Megatron's rebirth, when the Decepticons venture deep into the ocean to revive him, the Navy crew tracking them reads five contacts. When they get down there, they tear apart one of the robots for parts to rebuild Megatron. Then as they rise to the surface, the same Navy guys say they spot six contacts. The little "Doctor" robot popped out down there, but he's about a third of the size of a person. Would he have shown up on sonar?

4. That reminds me: even if I were to forgive the Doctor's German accent -- and director Michael Bay is asking me to forgive a lot of ridiculous accents -- why would a robot need glasses? He has little lenses that flip in front of his mechanical eyes. Couldn't he just get his eyes adjusted? You'd think with all the laser guns, someone could perform a Lasik procedure.

5. Apparently, Transformers can look like people now. How? And how is it that even though the robo-girl (Isabel Lucas) is made of metal, she can still straddle Sam without crushing him. And if Bumblebee knows something's wrong with her, why does he spit antifreeze at her instead of telling Sam? Yes, his voicebox is broken, but wasn't it fixed at the end of the last movie?

6. The Fallen is the last of the Primes, since they all sacrificed themselves to stop him from destroying the sun. But then he says that Optimus is a descendant of the Primes. First, Transformers have kids? And second, how could he descend from them if they were all dead? And if the Fallen could only be destroyed by a Prime, why didn't the originals just gang up on him back in the day? And what makes Optimus so special, anyway? Megatron beat him earlier, but all it takes is a few spare parts from creaky old Jetfire for him to take out the Fallen?

7. Sam, Mikaela, and Simmons (John Turturro) go to the Smithsonian Air and Space Museum in Washington D.C. to find Jetfire. Then they walk out the back onto a wide open field with old planes and mountains in the distance. When did the National Mall start to look so much like to Tucson, AZ (where they really filmed that scene)?

8. The geography is just as bad when they go to Egypt. The stone city of Petra in Jordan is over 250 miles away, over mountainous terrain, with few paved roads and the Israeli border between them, so how can they drive from one to the other in a couple of hours. And the Pyramids are said to be shooting distance from the Mediterranean, but they are actually well over 80 miles inland. Even if the Navy ship had a secret rail gun, and even if the captain would take an order to fire from a former agent of a government branch that no longer exists (over a walkie-talkie that inexplicably starts working again), how could it hit a moving target from that distance?

9. Sam briefly dies and goes to Robot Heaven. Robot Heaven?!?!

10. Where does Sam's bandage come from? What about his extra sock? Why does Sam's roommate not contribute anything at all? What was the Fallen doing for those thousands of years Megatron was frozen in ice? How does one satellite receive transmissions from everywhere on the planet? Why does Wheelie hump Mikaela's leg? Why do we have to see John Turturro's thong? Why are robots who join together to become Devastator also seen fighting the Army at the same time? Why does the government want only our military fighting Decepticons when our weapons seem unable to make so much as a dent on any of them? Why did the ancient Egyptians build a pyramid around the sun-destroying machines instead of just breaking it? Why is the Matrix of Leadership bigger in the Fallen's hand than in Sam's? And how do Mikaela's pants stay so clean?

Update: Below are one possible set of answers to the various questions asked above by Bruno. I thought they were good and logical and might help others in clearing up some things.
Question 3:
I believe the Navy is tracking and looking for the energy that ENB's emit.

Question 4:
His lenses are part of the alt mode - the microscope. It's common to see doctors with magnifying lenses when they do surgeries, and the Doctor was about to "extract" Sam's Brain to have the knowledge of his mind.

Question 5:
Part 1 - Apparently, Transformers can look like people now. How?
The pretender is a robot that looks like a human. In the Movie Prequels (HQs), while Sam is in the bedroom with Alice, Leo is in the living room watch tv and sees an advertisement of a new fun park (like disneyworld) and he sees a human sized doll that looks exactly like Alice. So, the pretender scanned the doll and transformed in a human.
Part 2 - And how is it that even though the robo-girl (Isabel Lucas) is made of metal, she can still straddle Sam without crushing him.
Alice, like the other decepticons, wanted what was in Sam's mind. So he must be alive to allow the Doctor to do his job.
Part 3 - And if Bumblebee knows something's wrong with her, why does he spit antifreeze at her instead of telling Sam?
When Bumblebee spits antifreeze at Alice he doesn't know she is a robot. He only do that because Sam is "cheating" Mikaela. During the entire scene, Bumblebee plays musics that focus on the cheating part.

Question 10:
Part 1 - Where does Sam's bandage come from?
When Sam crashes after the space bridge scene, he injures his hand and Mikaela put a bandage on it.
Part 2 - What about his extra sock?
Sam took one of his socks to put the ashes of the matrix inside. He doesn't have a third sock!
Part 3 - Why does Sam's roommate not contribute anything at all?
Leo doesn't do a lot in the movie but what he does is crucial to the storyline. Thanks to him, Sam and Mikaela meet former-Agent Simmons, aka RoboWarrior, and meet Jetfire, an autobot that helps Sam and Optimus Prime.
Part 4 - How does one satellite receive transmissions from everywhere on the planet?
In this question we see how stupid the person who wrote this is. We have a worlwide system of satellites that cover the entire planet. The GPS (Global Positioning System) for example.
Part 5 - Why does Wheelie hump Mikaela's leg?
It's called comedy!
Part 6 - Why do we have to see John Turturro's thong?
In the first movie, he has a shirt with a superman-ish symbol with S7 on it and boxers that match. In this movie, Bay wanted to push a little more on that.
Part 7 - Why are robots who join together to become Devastator also seen fighting the Army at the same time?
It's like the toys. They are diferent characters. So, we could say that there are 2 demolishers (1 dies in the beginning and 1 to form Devastator), 2 Scrappers, 2 Mixmasters ...
Part 8 - Why does the government want only our military fighting Decepticons when our weapons seem unable to make so much as a dent on any of them?
First, the government doesn't want that. It only askes if the Decepticons are in Earth beacause of the Autobots. Second, it's Optimus Prime that doesn't want to share cybertronian technology with humans (he explains that in the movie). Third, the military do have weapons to destroy robots. Think: what killed Devastator???
Part 9 - Why did the ancient Egyptians build a pyramid around the sun-destroying machines instead of just breaking it?
The ancient egyptians lived around 3000 a.C. Do you think they had any techology that could destroy the sun harvester?