Executive Meddling: Tons and tons and tons, relating to marketing and the usual reasons. Recent example: the Grand Finale to Simon Furman's Myth Arc comic series was cut from 12 issues to 4 so that IDW could publish All Hail Megatron instead.
Once per series:
Optimus Prime learns how to fly: G1, Beast Wars, Cybertron, Animated, Revenge of the Fallen, Prime
Megatron becomes Galvatron: G1, Robots in Disguise, Unicron Trilogy (and we mean every subseries of the Unicron Trilogynote Done for trademark reasons, according to Aaron Archer. It wasn't as much of an issue in Japan: Armada Megatron/Galvatron was Micron Legend Megatron/Megatron Super Mode; Energon Megs/Galv was Super Link Galvatron/Galvatron General; and the Cybertron version was Galaxy Force Master Megatron/Master Galvatron - Takara didn't originally intend for Galaxy Force to be in the same continuity.), Age of Extinction
Starscream comes back from the dead: G1, Beast Wars, Unicron Trilogy, Animated
Someone makes an evil Optimus clone: G1, Robots in Disguise, Energon, Beast Wars Second, Prime, Age of Extinction note When the humans in Age of Extinction make Galvatron, they specifically say that they're designing him to look like Optimus Prime; Galvatron keeps reprogramming himself to resemble his old body. He keeps Optimus' truck vehicle form though.
Inconsistent Dub: The Latin American and even the European Spanish dubs, All the way: Due to the fact Hasbro wanted to dub the Spanish versions in the U.S. for having more control about the dubbing (This is was during G1, the animated movie and the Japanese Anime versions, mind you) , all the Spanish language versions (including the European one) were sometimes dubbed by a Spanish-language studio in Los Angeles. The main problem with this approach is, due of consideration about the Spaniard viewers, especially in the Anime versions, some series were dubbed using the European Spanish dialect, but keeping the local accents intact: Not only the Latin American viewers had to tolerate a very fake Spaniard accent, but the Spaniards had to tolerate a ridiculous Spaniard dialogue with Mexican and Central American accents.
In fact, Mexican voice acting studios only dubbed a very small amount of Transformers stuff: The Beast Wars/Beast Machines series, Prime, Robots in Disguise and the live-action films. Other countries that dubbed the rest of the TF series were: Chile (Animated) and Venezuela (The Unicron Trilogy).
While the Mexican dub of Beast Wars was pretty good, it was panned for changing the names of all the characters to Spanish equivalents. This was corrected later in Beast Machines' dub.
What Could Have Been: Many, many toys and concepts end up being discarded - from G1 alone, we have characters originally being named differently (e.g. Swoop was to be named "Divebomb" before the name was later repurposed for the Predacon bird), a planned Unicron toy and two planned Arcee toys for the original toyline, an axed rerelease of the original Megatron toy in a blue/orange deco (dubbed "Lava Megatron" by Hasbro and "Safety Megatron" by fans), two Megatron triple changers (one that switched between Megatron, Galvatron and a gun◊ and another between Megatron, Skywarp and a plane◊ and many, many more. See here for more.
Nightbeat, a C-list character whom Furman brought to the forefront by making him a Film Noir-style Hardboiled Detective. In the current IDW-universe that Furman is helping to write, he killed Nightbeat off fairly early on so fans can know that Anyone Can Die, even his own favorite character. He did something similar in the G2 comics, killing off Nightbeat as a self-inflicted Player Punch.
Interestingly! The two are now considered to exist in the same multiverse. Albeit with the Go-Bots universe being very, very distant from any known Transformersverse. The only Gobot who has any sort of impact at all is Bugbite, who has since become a Decepticon.
Something interesting of note: While a number people claim to have memories of Optimus crumbling into dust after death in the Generation One Movie, he did not actually do that - it was the Armada Optimus who crumbled into dust on death. They may be confusing Optimus' death with Starscream's - 'Screamer did crumble to dust when dying.
Megatron almost had a different name. When the writer of the initial Transformers fiction came up with the name, it was shot down by Hasbro, as they felt it conjured up images of nuclear weapons. He then reminded Hasbro Megatron was supposed to be the Big Bad and the name was approved.
Similarly, Starscream was originally named Ulchtar in Denny O'Neill's original treatment for the comic book, but Bob Budiansky changed it.
Dawson Casting: Shia LaBeouf was 19-20 while filming and Megan Fox was 19, both playing high school juniors. Bay mentioned that he was initially not interested in LaBeouf because in his movies immediately prior he had grown a goatee, making him look too old to play a teenager. Seeing him clean shaven convinced him otherwise.
The human/Transformer hybrid known as Alice is being called "Deceptislut".
"Bayformers," while starting as a pejorative (and to some still is) has gone on to be an affectionate name for the series and the robot designs in general.
Sadly, the designs are one of the main reasons why some people hate the movies, from Fan Dumb (Prime having a mouth, and the robots not looking exactly the same as G1, the former of which being serious Fan Dumb since he's able to activate a mouthplate to take on the "mouthless" look), to good reasons (many minor Decepticons look the same, although minor Mooks in Transformers always have).
As we noted above, Frank Welker using his unmistakable Dr. Claw voice for Soundwave once more (He also uses it in the French and Italian dubs of the film, confirmed by Welker himself). He also plays Megatron in the first two movie games; Grindor, Devatator, Ravage and Reedman in Revenge of The Fallen, and Shockwave (and through an audio/animation error, Barricade) in Dark of The Moon. In Age of Extinction, he reprises his role of Galvatron, and since he's Megatron in a new body, he's technically also reprising Megatron in the films proper!
Also, as noted above, Peter Cullen reprises the role of Optimus Prime.
Following Cullen in Japan, Tessho Genda once against voiced Optimus/Convoy.
They were going to put a transforming aircraft carrier (which partially inspired the toy-only stealth battleship Depthcharge), but the scale would have been extremely awkward to animate — as in, it would have likely been able to walk on the ocean floor while keeping its torso above water.
Fan favorite Springer was scheduled to be in the movie as an Osprey twin rotor helicopter, with two toys released based on the design. The guess is he was dropped because the Osprey design would make him absolutely tower over near every other robot (at about 60 feet tall) and give Devastator a run for his money.
The very first non-movie character to get a toy was Wreckage - a Decepticon with an APC altmode based on an ILM design that eventually went unused.
Both the twins and Arcee were apparently supposed to combine into a larger robot form. The cycles' version got far enough to make it into the toyline, the Twins...not so much (though the ice cream truck did).
The studio initially requested that they try and make it so the robots don't talk at all, fearing it would come across as silly. Both the writers and Michael Bay knew that despite the requisite cries it was ruined for any changes, the fans would absolutely crucify them if the robots didn't talk.
Soundwave was to appear in the first movie, his role being an inverted Composite Character of Frenzy and Barricade. Since there would be major size changes involved (he would go from a robot to a radio to a humvee), he was split off. At first, Frenzy was to be named "Soundwave", but the writers changed it because they felt the character was too different from all the other Soundwaves. Another attempt at working him in eventually turned into Blackout and Scorponok.
The various adaptations of ROTF feature a different ending than the movie itself, where Megatron, having found out that The Fallen had been lying to him and manipulating him all this time, leaves his master to die and flies back to the Nemesis with Starscream to awaken his new army.
James Arnold Taylor was originally cast as the Fallen, but was later replaced by Tony Todd. He did keep the role for the video game though.
Peter Cullen reprises his role as Optimus Prime for the Michael Bay films, but he does not reprise his role as Ironhide. Frank Welker returns as the voices of Soundwave and Ravage, but his other characters (Megatron, Frenzy and Laserbeak) have new actors. He was going to portray Megatron once more, but Michael Bay decided that Welker's voice didn't match his vision for Megatron.
Amusingly, Frank Welker's brief lines for Shockwave in DOTM sound an awful lot like his G1 Megatron voice.
According to the family tree that Sam presents in the first film, the Witwicky family consists of two generations of inbreeding. This might be a case of Critical Research Failure on Sam's part though.