The Fallen was over 20,000 years old, at least as old as Jetfire (who was falling apart), and would not come to Earth until Optimus was dead, implying that he was somewhat afraid of Optimus, so it is somewhat justified within the movie. Still, it was quite a disappointment to see the guy the comics have always presented as about midway between Megs and Unicron on the Oh, Crap!-ometer go down so easily.
Alternately, it could be interpreted as a Curb-Stomp Battle. After all, he was doing impressively until a Jetfire-amplified Optimus Prime arrives on the scene.
Alternative Character Interpretation: The scene early in the movie where the Autobots and N.E.S.T. are in Shanghai attacking Decepticons who were doing nothing but minding their own business has led some people to consider that the Autobots (or at least Optimus) are not as heroic as the movie intends them to be seen as.
Ass Pull: Some of the film's developments are pretty hard to swallow, to say the least.
Only just finding a shard of the AllSpark attached to his shirt a full two years after killing Megatron.
Simmons just happening to know of a weapon that could take down Devastator, which just happens to be on a nearby warship.
Scorponok just happening to show up during the battle in Egypt where he mauls Jetfire before he's unceremoniously disposed of, having apparently managed to avoid detection for two years after his defeat in Qatar.
The infamous sequence where the Primes resurrect Sam and repair the Matrix comes completely out of nowhere.
The ability of the Transformers to teleport, which we see from both Jetfire and the Fallen is not explained or an ability seen from equally powerful cybertronians like Optimus or Megatron.
While cool, there is zero buildup to the concept of cybertronians being able to graft parts from other cybertronians onto themselves.
Badass Decay: Megatron got this slightly; while still very powerful, he's now The Fallen's Yes-Man and is not quite as unstoppable as before. Starscream, on the other hand, was the character who definitely got this, becoming a complete Dirty Coward.
Base-Breaking Character: Optimus fell into this. He remained the most popular Transformer in the series and is one of the biggest badasses in the movie, but quite a few fans took issue with his more savage battle tendencies introduced in this movie, which contradict the relatively pacifistic nature of the Optimus Prime character in most media. A third group of fans liked this incarnation more, happy that the movies were willing to make some changes with the usually infallible role that Optimus usually takes.
The scene with the Allspark fragment from the first film falling into the kitchen, turning his kitchen appliances into destructive feral Transformers, a fight ensues, the house is destroyed. Afterwards, this scene is never mentioned again, despite likely being used to establish the power of just one Allspark fragment.
Even worse, after the scene Sam goes right back to insisting he doesn't need Bumblebee's protection anymore.
Counterpart Comparison: Alice the Deception Pretender is very nearly the T-X from Terminator 3: Rise of the Machines. They're both shapeshifting robot assassins with built-in weapons whose human disguise is a beautiful, sexualized blonde woman; Alice's robot form even resembles the T-X (something several viewers pointed out, including CinemaSins in their review of Transformers 2, which can be seen here; their comment is at the 9:33 mark note An earlier comment in the video directly mentions shapeshifting liquid metal, so that could be a nod to the T-1000 from Terminator 2 as well).
Critic-Proof: Despite a 20% Rotten Tomatoes score and extreme hatred toward the film on various movie sites, the film still grossed over $800 million worldwide, and (with only a 2D release, no less) ranks among the few movies to make over $400 million in the U.S./Canada market; indeed, it was the 2nd highest grossing film of 2009 (behind Avatar) in the United States, and the 4th highest worldwide, and adjusted for inflation is the 81st highest grossing movie of all time. It has also received a solid Cinemascore rating and Rotten Tomatoes user rating, and has sold generally well on DVD and BluRay.
There's debate over whether Skids and Mudflap were really that bad — many people point out that if Michael Bay actually possessed a decent sense of humor, they could have been Actually Pretty Funnyand badass. As it was, all their humor was based on derogatory stereotypes.
At least some of those are countered in the novelization. For example, Skids' and Mudflap's line that "They don't do much reading" to justify why they couldn't read Cybertronian symbols (when they're, you know, robots who have computers for brains) is changed to that they can read, but the symbols are from the language of the Primes, which they don't know and is separate from the standard Cybertronian language.
While this is largely considered the worst Transformers live-action film by critics and a good portion of the fanbase (due to its slapdash nature, over-used humor and underdeveloped plot), a good number of Transformers fans consider it to be the best of the trilogy, owing to it being the only one that feels like Transformers (The first movie had a far greater focus on humans - to the point of the Transformers almost being a secondary plot, while the third felt detatched from the mythos, changed several characters' core personalties and felt more like a Star Trek movie to some people).
In retrospect, with its lower-quality writing and cheesy plotline, it does feel a lot more like the old 80's cartoon.
Memetic Mutation: Optimus' line "Give me your face!" right before tearing the Fallen's face off.
Misblamed: Some accused Michael Bay of holding an anti-Barack Obama agenda, since he is specifically mentioned as being the president, and the government officials go from being generally cooperative (albeit in over their heads) in the last film to being complete jerkwads in this one. However, as Bay pointed out, the screenplay was completed and filming began at the start of 2008, before he or anyone else involved knew that the Democrats would nominate Obama (Hillary Clinton was still the favorite for their nomination at the start of 2008, albeit by a slim margin), much less that he would out-poll all other presidential candidates. Additionally, Obama is only mentioned in a brief line that was clearly dubbed on in post-production, which could easily be swapped out for one mentioning John McCain with no real effect on the movie.
The embarrassing ease with which Optimus is able to hand Megatron his ass right before the forest battle, while trash-talking him, is this to a lot of people. Then, during the otherwise spectacularly rendered forest battle itself, there's a very glaring animation shortcut, where, for a split second, Megatron goes from charging furiously at Optimus to strolling complacently. It's partially obscured by the nature of the shot, but many sharp-eyed viewers found it hilarious.
Really, most of the movie can fall into this. The Vulgar Humor, bizarre characters and dubious plot completely undermine any sense of gravitas or solemity it tries to convery, and it ends up becoming hilarious instead.
Narm Charm: "Give me your face!" Only Optimus Prime can make such a silly line sound threatening.
Never Live It Down: Before the release of RotF, the first Transformers movie was pretty well-liked but still debatable (even being nominated for a People's Choice Award). After the release of RotF, people started lumping the first movie together with its sequels as one of the "worst action movies of all time", and generally feel that any sequel released will inevitably fall into the same pit of putrid quality (including the two that have already been released).
Michael Bay himself has yet to fully separate himself from the reputation this film has gained, as it helped cement what audiences and critics disliked most about his directing style.
Movie Prime has yet to live down his "Give me your face!" line. Not helped by his tendency to target heads in the sequels.
Older Than They Think: The idea of Transformers like Alice who can turn into humans is actually nothing new. The Pretenders first appeared in Generation 1, and both sides had them. (Although in that version, a Pretender's disguise was more like Powered Armor which could actually fight independently of the Pretender once it revealed itself.)
Romantic Plot Tumor: The Sam and Mikaela subplot is considered very annoying and distracting, particularly due to Mikaela insisting Sam say he loves her while the fate of the world hangs in the balance. The next film would reveal the characters broke up anyway, making the subplot feel even more unneeded and pointless.
Though he certainly looked awesome and had Tony Todd's performance gong for him, between having zero motivation or characterization, a bizarre grab bag of unexplained powers, an awful, anticlimactic clusterfuck of a fight to his name, and nothing shown in the way of actual transformation, there's a reason the Fallen himself is widely considered to be the worst Big Bad of any of the four films. Even Bay himself admitted that the Fallen was "kind of a (expletive) character" in an interview.
Sam's parents and Leo are the worst characters in the series for being a burden and annoyance. They have no significant influence to the plot.
The Pretender Alice, whose presence in the plot feels rather forced, exacerbating the already contentious Sam and Mikaela subplot, and the film having difficulty deciding if it wants her to be scary or funny. The fact that a concept bringing in as much Paranoia Fuel as her, did actually have the potential to be something very dangerous and interesting, certainly doesn't help the disappointment over how she was used as just a romantic plot device either.
Seinfeld Is Unfunny: When ROTF was released, critics hated it, but general audiences were kinder to it and even defended the movie. Now, after twosequels full of deliberate attempts to correct ROTF's flaws, the movie is far less popular with general audiences, and is much more widely hated for turning the Transformers series into the critics' favorite punching bag.
Sequelitis: Is infamously the second worst-reviewed movie in the series, and is widely considered one of the worst mega-blockbusters of all time. It is often credited (along with G.I. Joe: The Rise of Cobra) with causing the genre to no longer be taken seriously in Hollywood.
Other quality issues aside, this movie does contain the famous forest battle, generally considered to be the series' best fight scene.
Whatever you may think of Devastator himself, his introduction falls squarely under this.
Optimus forging with Jetfire's remains before confronting The Fallen is also worthy of note.
Sophomore Slump: One of the biggest examples in film history. Just try and find anyone who prefers this movie over any others in the series.
Special Effects Failure: It's plainly obvious that the rendering and animation of the robots during all of the desert scenes, with the notable exception of Devastator, aren't up to par with the rest of the movie. The scenes that take place on Saturn's moon and in particular, the one where Starscream backs into a hatchling's pod, also look unfinished. It's particularly unforgivable when you consider Revenges budget outstripped its predecessor's by $50 million. Appropriately, while the first and third movies were nominated for the Visual Effects Oscar, this one was not. See Narm above for another infamous example.
The titular Fallen. He's voiced by Tony Todd, the Greater Scope Villain to all of the Decepticons, pretty savvy when it comes to picking his spots, and evidently quite a winner in the Superpower Lottery. Sadly, he also turns out to be a Flat Character with the barest minimum of screen time, not to mention his extremely glaring Forgot About His Powers moment against Optimus that ultimately robs viewers of a satisfying final clash. And reportedly, even Word of God ultimately regrets how he's turned out.
Arcee, Chromia, and Elita-1 as well. They get even far less screen time and dialogue than the aforementioned Fallen, Elita-1 is abruptly and cheaply Killed Mid-Sentence during the finale, and both Arcee and Chromia subsequently suffer What Happened to the Mouse? statuses. Not helped at all by Michael Bay confirming all three of them to be dead and that he killed them off out of sheer hatred of the characters.
Alice, a Cybertronian Pretender who could perfectly mimic any human. She could easily have become a threat had she assassinated and imitated someone like a military general, where she could have actively worked to worsen human/Autobot relationships and sabotaged NEST from the inside. But instead, she was only used as a cheap device for the Romantic Plot Tumour.
Uncanny Valley: The Autobots and the Decepticons taking on increasingly human-like features as part of their primary modes; for example, the Fallen's "beard" and head resembling an Egyptian headdress. This would later become a norm for the sequels.
Perhaps more disconcertingly, Skids and Mudflap, who along with their already stereotypical behavior were widely accused of mimicking blackface.
Finally, Devastator's wrecking balls.
Values Dissonance: The entire reason why Skids and Mudflap were later removed entirely from the later films.