My apologies if I'm repeating points made by others. I have not read every post in this thread.
But onto the list...
-"Leadership" in Bayformers language means "being able to blow up the sun" because that's all the "Matrix Of Leadership" was made for... blowing up suns... But I guess "Matrix Of Leadership" is catchier than "Matrix Of Supernovas"
-The Allspark should have been left alone because anything it touches and brings to life is violently evil.
-The Fallen is really lazy since he sat for thousands of years before the other Transformers showed up. Remember Bumblebee was the one who signaled them in the first place in the first movie.
-"Top Secret" security apparently is still not important enough for security cameras.
-Autobots hunt down and murder Decepticons, even when they apparently aren't doing anything. They seem to not care how many humans get caught in the crossfire either. When they catch their targets, they just cap them in the head, without any thought of offering mercy. And they're supposed to be the good guys.
-Some middle aged housewives apparently still have no idea what pot is, even though they would have remembered the 60s and 70s.
-Aliens in other galaxies must utilize the SR-71 body style, because Jetfire has no recollection where Earth is... despite being in the form of a decades-old Earth jet.
-Covert operations still involve deploying in public, with vehicles that have your operation's name plastered all over them
-Women go wild for geeky guys who, despite being an item for 2 years, still never say they love her
-Robot Gods have power over whether humans die or not, and are big fans of The Lion King
-When trying to snuff out the one human with the key to unlocking your goal of world destruction, don't bother targeting him from the distance. Just make a high-tech robot slut, enroll her in his college classes, and have her follow him around for days. He'll eventually fall for it, even if she misses multitudes of opportunities to kill him without anybody noticing.
-When trying to steal the one remaining key to the above world destruction, don't send one of your nearly indestructible soldiers who can transform into a great machine of war.... send a toy truck with questionable loyalty who is one tenth the size of a human.
-Optimus Prime is the fastest of all the Autobots, despite being a truck. This is evidenced by no other Autobots being around during the fight following the rescue of Sam.
-Bumblebee must have some sort of robot learning disability, because he was able to talk at the end of the first movie, but is reduced once again to speaking through radio clips again come this one.
-In the Cybertronian numbering system, "twins" mean "three".
-Megatron forgets his priorities sometimes. When resurrected in the first movie, he doesn't bother with trying to get back in touch with his master, he just wants the cube.
-The Allspark is very moody. A fragment of it gets Sam all freaked out. But yet he could carry around the entire cube with no problems in the first movie. Not to mention the cube kills Megatron... and then later is used to resurrect him.
-Even though your race has mastered interstellar space travel, always keep the key to the aforementioned world destruction on the same planet. Then have you and all your friends dies around it. Nobody will go looking for it on the same planet. Taking it to another star system is just ridiculous.
-When you've failed at world destruction, don't bother traveling to another planet to destroy it and feed off the energon. Just wait around for 12,000 years since you clearly have enough energon in your system already to live such a long time. Somebody is bound to pick up where you left off.
I may come up with more, but that's all I got for now.