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.
The Fallen was over 20 thousand years old, as old or older than 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.
Which is, to be quite honest, a bit like saying "Well those particular Nazis weren't gassing any Jews at that particular moment, and yet those vicious Allied soldiers still killed them anyway, what monsters."
Badass Decay: Megatron and Starscream. Megatron's case is more arguable than in the following film, however, since he still engages in quite a bit of genuine combat and manages to kill Optimus (though he gets better). Starscream, meanwhile, has been reduced to a complete joke.
Big Lipped Alligator Moment: 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.
Critical Dissonance: Despite a 20% Rotten Tomatoes score and extreme hatred toward the film on various movie sites, the film was still a huge hit. Making over 800 million worldwide and is still one of the few movies to make over 400 million domestically (with only a 2D release no less). It has also received a solid Cinemascore rating and Rotten Tomatoes user rating, and has sold generally well on DVD and Blu Ray.
Hype Backlash: Presumably why this movie was hyped as "the worst movie of 2009" to some and beat out Dragonball freaking Evolution and similar worse-reviewed flops at the Razzies.
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 one that's already been released).
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 co-operative (albeit in over their heads) in the last film to being complete douchebags in this one. However, as Bay pointed out the screenplay was completed and filming began at the start of 2008, before they even knew that Obama would be the Democrat nominee, much less president.
There's debate over whether Skids and Mudflap were really that bad - many people point out that if Michael Bay actually posessed a decent sense of humour, they could have been Actually Pretty Funnyand badass. As it was, all their humour was based on derogatary 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.
Special Effects Failure: It's plainly obvious that the rendering and animation of the robots (Bar Devastator) during all of the desert scenes aren't up to par as the rest of the movie. Also, the scene were Starscream backs up into a hatchling's pod looks stiff and unnatural.