These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Dylan Gould: Is he a Jerkass Woobie who was unfortunate enough to inherit his dad's allegiance with the Decepticons, or simply a Dirty Coward who wanted to be on the "winning" side? His Moral Event Horizon crossing indicates that he's more so on the latter.
One is also reminded of Saren Arterius, another organic who made a desperate deal with Humongous Mecha From Space in the hopes of saving some remnant of civilization. This is a bit of a stretch, though, as Gould does not express any such sentiment.
Megatron: Was he earnest when he wanted a truce, or did he just want to reclaim his role as Decepticon leader? How you interpret this will also say something about Optimus's following actions.
Did Megatron actually deserve the benefit of the doubt, even if he was sincere? Or is this a case of The Farmer and the Viper?
On the other hand Optimus probably remembered what Megatron did in the last film.
The Autobots as a whole, continuing from the previous movie where they attack Decepticons who are just minding their own business. Here we see the Decepticons aiming to take prisoners (only deciding to execute the Autobots after being talked into it by Dylan), something the Autobots never consider doing with Decepticons they defeat. Decepticons are concerned about the wellbeing and future of their race (Megatron's taking care of children at the beginning, and the whole attempts to restore Cybertron). This paints a weird portrait of the Autobots, who seem like sore losers about losing the whole war, and would rather drive their own species towards extinction than accept their defeat and let the Decepticons rebuild Cybertron. It's true that most of these plans for rebuilding were at the Human race's expense, but frankly Megatron's hatred of humans is understandable: The first we did is dig him out, keep him paralyzed, then vivisect him For Science!! (And if you factor the Novelization or the common Handwave for him knowing English when he awoke... He was conscious through it all). It becomes easy to see the Decepticons as Well-Intentioned Extremist and the Autobots as borderline sociopaths. And that is without even getting into the Autobots involving themselves in human politics at the behest of a single country...
Although this interpretation misenterprets a few things of the movies: Optimus makes it pretty clear the War is lost (in the third movie, he outright says such to Sentinel) and that he has no hopes or intentions of winning it, his focus is keeping humanity from meeting the same fate as his race did: In the first movie, for example, he attempts to sacrifice his own life to save humanity, even though that would mean the Decepticons would win. The second movie also shows The Decepticons planned comitting genocide here long before the war even began (With The Fallen and all), not to mention seeking to destroy/enslave the entire human race because a bunch of agents from one government from a one country imprisioned you (without the rest of the country knowing it, mind you) is a pretty big overreaction. On the politics matter, the label of the scene said "ILLEGAL nuclear facility", meaning it probably belonged to some guerrila warlord and not a government.
It also misses the fact that outside of divine intervention (All Spark) or destruction on a scale larger than Cybertron itself, Cybertron is already dead. 'Winning' and 'restoring the world' wouldn't actually accomplish anything since there's nothing left to restore. While the Autobots may not have any particular need or desire to restore Cybertron, they also realize that the 'war' at this point is essentially pointless in-fighting. There's no new Cybertronian life being born or created so 'bots and 'cons are doing little more than driving themselves to extinction. Megatron doesn't want to restore Cybertron - he wants to win and he wants a place to rule; Cybertron is just a convenient rallying call. A more realistic approach if he truly wanted to help the Cybertronian race would be to stop fighting and start figuring out a way to bring his race back from extinction - colonizing Mars for instance.
Angst? What Angst?: By the end of the film, the Autobots seem pretty held together despite the fact that they just possibly lost Cybertron forever. Then again, they had already more or less accepted that Cybertron was irredeemable by the end of the first film, so it may not be that big a deal.
Base Breaker: Sentinel Prime tends to divide moviegoers into two camps, of which the first sees him as a surprisingly complex character with a really cool design and one of the biggest Badasses of the entire franchise, while the other hates him for brutally executing Ironhide and sidelining Megatron as the Big Bad.
Megatron himself veers sharply into this territory. While his Badass Decay is generally agreed to be at its worst here, the fact that it's very much an Invoked Trope that fleshes out his character more redeems him in the eyes of some. In addition, being forced to sit out of direct combat allows him the opportunity to mastermind the impressive Batman Gambit that makes up the first half of the film. That said, the fact that Optimus takes him down with the absolute greatest of ease is generally seen as a slap in the face to the character, especially considering that the alternate ending is seen as a far more redeeming and rewarding one for him that reestablishes him as a Badass and rounds out his Character Development in the movie. Despite this, Transformers: Age of Extinction shows why DOTM has the ending that it does - it's so Megs can stay evil and return as Galvatron - which, while not as "clean" as the alternate ending, at least allows him to persist as the franchise's flagship villain.
Megatron's aesthetic, particularly his altmode and cloth cloak, is itself a Base Breaker. Reactions range from "very cool in a rugged sort of way" to "does a good job capturing his fallen-by-the-wayside characterization" to "silly as hell."
Complete Monster: Dylan Gould has spent his adult life aiding the Decepticons in their plans on Earth (saying they're "clients" he "inherited" from his father) and assisting them in their takeover of Chicago, which sees thousands of people gunned down in the streets, all to ensure that he'll be spared. This could just be written off as him being a Dirty Coward, but the moment that has him cross the line further is when several Autobots have been captured and Gould humbly suggests to Soundwave that they shouldn't be taking prisoners at all. When the pillars have been shut off, meaning the Decepticons' plan has been foiled and he has the option to defect to the good guys and possibly be spared, if jailed, he chooses to reactivate the pillars for no real reason. This is most sensibly interpreted as being done out of sheer spite, even at his own expense, considering the Decepticons have all their human minions killed once they cease to be useful and will likely do the same to him.
The military characters have been considered, by a large few, the more interesting characters when compared to Sam and his useless human supporting characters.
Harsher in Hindsight: The film ends with Optimus narrating that the Autobots will never abandon Earth and the humans. As shown in the fourth film, the humans not only no longer trust them, but paramilitary groups are actively hunting them down.
Sentinel Prime laments to Optimus that humanity does not treat them with respect, as on Cybertron they, the Primes, were Gods. But on Earth they are "merely machines." Optimus disagrees on principle, as he has allied himself with many noble humans. Come the following film, paramilitary groups have no qualms about targeting Autobots or Decepticons alike, as they are more interested in replicating their scientific properties rather than acknowledging them as actual living beings. The For Science! character Joshua even tells Optimus that they are just metal. At this point Prime himself is PISSED.
Also, you know, blowing up the entire Autobot spaceship with them inside.
Moral Event Horizon: Sentinel Prime brutally killing Ironhide. Also, the Decepticon's genocidal attack on Chicago in the same movie might have finally driven home the point that yes, the Decepticons really ARE evil.
Laserbeak: "Is your daddy home?", said right before killing the poor girl's parents right in front of her.
When Soundwave brutally executed Wheeljack after the Autobot had surrendered and was begging for mercy, you knew he deserved everything that happened next.
Any sympathy for Dylan leaves when one sees the lengths he's willing to go to ensure that he isn't harmed by the coming Alien Invasion. Like when he reassures himself that he's safe... while watching hundreds of innocent civilians be slaughtered by the Decepticons.
Most Annoying Sound: Sam's constant screaming. He did his fair share of it during the first two movies, but that was understandable since giant freaking robots were constantly trying to kill him. In this movie, just to name one example, he spends the better part of a minute screaming aloud because his car gets caught in a security pen outside the Autobot base.
Replacement Scrappy: This was anticipated with Megan Fox / Mikaela's departure and Rosie Huntington-Whiteley brought in as a new character, as a lot of fans appreciated that Mikaela wasn't a useless screaming love interest and disliked that Rosie was a Victoria's Secret model with no prior acting experience. The potential anger was ebbed slightly when Rosie's character was named Carly after the G1 character and Rosie herself commented on being proud of being a part of the franchise. But to a lot of people's surprise both Rosie's acting and Carly herself turned out better than expected, as Rosie wasn't a rehash of Mikaela as a blonde and she was consistently cheerful and friendly even through Sam's moody moments in the movie.
On the other hand, one hilariously vicious review said that Dark of the Moon is the only movie that could possibly make you miss the acting talents of Megan Fox.
It's also clear at times that the script was written as though Fox's character was still in it. For example, the fact that the government is comfortable with Sam bringing Carly into their secret Autobot command base without any prior approval is rather forcefully handwaved, whereas Mikaela would have had the same protection that Sam enjoys, since she was there for all of the events that Sam was present for.
Rescued from the Scrappy Heap: Wheelie was better received than in the second movie because A) no leg humping and B) he actually helps in the climactic battle. Along with his partner, the even more quirky Brains, they manage to liven up the mood without being too obnoxious.
On the other hand, that pissed quite a few of Starscream's fans off, attributing it more to Starscream suffering from Badass Decay than Sam having Took a Level in Badass.
They Wasted a Perfectly Good Plot: It's generally agreed that, like with the previous movie, the alternate ending depicted in the novel and comics where Megatron pulls a Heel-Face Turn and joins forces with Optimus to kill Sentinel, afterwards leaving for Cybertron to help rebuild it, is better than the movie's actual ending. It would have shown Megs get some of his old Badassery back and made his Character Development more obvious, showing that he was a Well-Intentioned Extremist all along who genuinely cared about restoring Cybertron and would even give up his evil for that end. One guesses that this may have been because Paramount wanted to leave him evil so that he can return as a villain for future sequels, which did happen after all in Age of Extinction.
It's shown in the third film that humans are aware of the Transformers, and that the Autobots are not well liked by the US population (being referred to as "alien mercenaries"). There are clear reasons for this dislike; the Autobots cause countless property damage in their battles, and there's the fact that the average US citizen has to worry about whether or not the car or machine near them is not a dangerous alien warrior. Sadly, the movie only touches lightly on this, and never really explores how the Transformers' known presence has affected the world at large.
This is ultimately subverted, however; promotional material for Transformers: Age of Extinction shows that humanity's attitude towards Cybertronians (particularly after Chicago's destruction) will play a big role in the next trilogy's Myth Arc.
Surprisingly Improved Sequel: It is up for debate, but the movie does aim to fix the problems that happened in the second film and fans were generally impressed with some of the story twists like Sentinels betrayal and Ironhides death, Gould's reveal as a bad guy and Carly convincing Megatron to retake his leadership of the Decepticons.
Take That, Scrappy!: Narrowly averted the film was going to contain a scene where Mudflap and Skids were killed off during Sentinel Prime raiding NEST. The scene, and their presence in the movie was cut for pacing. The scene does appear in IDW's comic book adaptation of the movie, playing the trope straight.
Uncanny Valley: Wheeljack/Que's face might seem a little too human-like for some viewers.
Most of the time they show their cg JFK's face out of focus. They focus on it one time briefly. And boy is it creepy.
There's also the CGI version of Sam as he swings around after stabbing Starscream in the eye. The CGI becomes noticeable when they show the close up of his face.
Take That: Several characters take little jabs against Megan Fox's character due to the actress falling out with Bay prior to the filming of Dark Of The Moon. In one scene Wheelie mentioned his dislike of Sam's ex, as she was mean. Things apparently began to fall apart after a magazine interview had Fox compare working under Bay to both Napoleon and Hitler.