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.
Accidental Innuendo: Padme: "My goodness, you've grown!" "So have you", says Anakin, his eyes fixed squarely on Padme's chest.
Alternative Character Interpretation: A lot of the romance subplot actually begins to make sense if you interpret Anakin as (un)intentionally using the Force to manipulate Padme's emotions, causing her to fall in love with him. This isn't actually too far out there because its not like we haven't seen Jedi casually Mind Rape people to get what they want.
Though the EU (especially the comics) don't take it as far as Mind Rape, they clearly present Anakin's obsession with Padme as extremely unhealthy, possessive, and dysfunctional. What is unclear is whether or not Lucas intended to imply this interpretation, or whether he was genuinely trying to write them as a romantic couple and that somehow fell through.
Alternatively, the awkwardness of the scenes also makes sense when you realize how incredibly sheltered Anakin and Padme's lives really are. Neither of them had any real relationship experience before - aside from Padme's brief summer fling when she was about twelve - and would have no real clue what they're doing. This would also explain how they never really looked past the hormonal fog and shared history to realize that they weren't really emotionally and mentally ready for a long-term relationship, never mind marriage.
Why she seems to somehow forget what Anakin did to the Sand People, including killing their children, between him telling her this and when he murders the Jedi Younglings in Revenge of the Sith. Though to be fair, a great deal of time passed between movies two and three, during which the Clone Wars raged. While it would seem hard to believe she completely forgot what happened, it can't be denied there was likely a lot on her mind prior to the attack on the Jedi Temple. Or perhaps, like everyone else, Padme just assumes that the Sand People are nothing but savage cannibals who go around brutalizing people for fun and thus viewed them as not deserving sympathy.
Hadn’t the Tusken Raiders just brutally kidnapped, tortured, murdered, and possibly raped his mother? After all, similar behavior never stopped women from falling in love with John Wayne in numerous Westerns.
Here's the problem with Sand People/Tusken Raiders: They're survivors of the cataclysm caused bythe InfiniteEmpirethat reduced Tatooine to a giant desert. As a result, they're extremely paranoid, violent and anti-technology, and will attack anyone using any of it, even a housewife caring for moisture vaporator(A machine to make water out of humidity). The only person who ever managed to talk with them was Revan, and that was because he used a translator droid; even then, they were extremely hostile. Padmé doesn't know any of that, neither does the rest of the galaxy. All she knows from the Sand People is that they're mindless desert savage tribe who, in her time in Tatooine from years ago to present time, tried shooting Anakin as a child while he was podracing, kidnapped and killed his mother, as well as cripping her husband and killing all rescuers, for no clear or good reason. It's not illogical for her to think they're Always Chaotic Evil, or Anakin; he grew up in Tatooine, and probably heard of the horrible things Sand People do. She WAS horrified by Anakin's act, but the mix of his mother's murder and the fact the Sand People seem to be nothing but monsters lessened the horror from the act (And unless you played the games, you'll also reach the same conclusion.). The Jedi Younglings are another thing entirely. They are kids, sentient and innocent, and Anakin killed them in cold blood when he didn't even need to. He could have just as easily taken them into custody and let Palpatine try and convert them to the Dark Side. Unlike the first time, Anakin doesn't have a good enough excuse.
The reason behind their savagery doesn't exist in the context of the movies. Unless they gave moviegoers a copy of Knights of the Old Republic, it's irrelevant (and besides, the game was released about a year after the movie). In the context of the film, they're a hostile race who cannot be reasoned with. I'd argue they're more akin to animals than to humans..
The Gungans choosing Jar Jar Binks as their delegate in the Senate was less reward and more a way to finally get rid of him.
Angst? What Angst?: As many fans have pointed out, Padme seems weirdly nonplussed about her lover openly admitting to murdering a village of Tuskens—including women and children.
Author's Saving Throw: Some fans suspect that Yoda training all Jedi as children was thrown in to fix the continuity issue of Qui Gon being Obi Wan's master in the last film, when he'd called Yoda "the Jedi Master who instructed me" in Empire Strikes Back.
Awesome Music: If you didn't think Anakin and Padme dialogue's showed they were in love, their theme "Across the Stars" hopefully did a better job of that.
Ensemble Darkhorse: Lucas apparently finally recognized Boba Fett's massive popularity with fans, so he retroactively gave the character a much more important role in the story and gave us Jango Fett, his father/clone who looks and dresses just like him but actually gets several awesome action scenes.
Unfortunately, having a set in stone backstory as part of the main story takes away a lot of Boba Fett's mystique. To say nothing of the Narm that comes from seeing him as a kid.
Harsher in Hindsight: Anakin's guilt over murdering the children of the Sand People becomes extremely disturbing after the next movie, in which we see one of his first deeds after turning to the dark side is killing younglings at the Jedi temple.
Also Anakin, when complaining of his nightmares, says he'd much rather dream about Padme. When you know what happens in the next movie...
Memetic Mutation: See the above Hilarious in Hindsight. Star Wars fans have noticed Django and Jango Fett's names have identical pronunciations and have created mash up photos of the twofranchises.
"Begun, the [X] wars have."
Narm Charm: Many found this to be the case, often due to crossing over into So Bad, It's Good, especially Anakin's "I hate sand" speech.
Part of why the "sand" speech is rather charming is the realization that Anakin is 19, has no experience with romance, and his childhood crush is standing very near him wearing an outfit that displays a great deal of "soft and smooth" skin.
Never Live It Down: Anakin hates sand. And loves Padme because she's not sand. Yeah, that speech really could have been written better.
Romantic Plot Tumor: At least to some degree between Anakin and Padmé. Probably made more glaring by some of their scenes being really toe-crunchingly awkward. While by no means the worst tumor in film history, being a Star Wars film is the reason that the trope was originally called "George Lucas 's Love Story".
Rooting for the Empire: Actually invoked by George Lucas. The movie introduces the sympathetic Clonetroopers, who save the Jedi and rout the movie's villains. Then comes the finale, and the movie reminds the viewers that they had been rooting for what will become The Empire by playing the Imperial March.
So Bad, It's Good: Hayden Christensen's acting, especially when he has to be romantic.
Take That, Scrappy!: Lucas finally admitted that Jar Jar was a horrible character, and in making him responsible* sort of; the plot point was going to happen regardless, Jar Jar just sped it up for enabling Palpatine's rise to totalitarian power, just wanted to give viewers one last reason to hate him. He later had a statue put up in his studio of Jar Jar frozen in carbonite, so at least he can laugh at himself.
They Wasted a Perfectly Good Character: An assassin who's also a shapeshifter? Awesome! (And also hyped in the pre-release publicity.) Sadly, Zam Wessel's ability to change her appearance is never actually used in any way whatsoever, even in a crowded bar where it would seem that looking like someone new (and taking your distinctive headgear off) might help you approach your targets. It was evidently more important to recreate the "disarming" from the Cantina Scene in Episode IV.
Throw It In: Nick Gillard mentioned that he had worked on developing a signature lightsaber style for Mace Windu but Samuel L. Jackson had already devised the very smooth and efficient style you see in the film. "It's Sam Jackson, he has a style all his own."
Uncanny Valley: Seen Temuera Morrison? Cool. Seen a million Temuera Morrisons in CGI? Yeah.
Considering the nature and purpose of the clone army, one could make a case for it being an Intended Audience Reaction - a million-strong Temuera Morrison army is never going to not be Uncanny Valley, and considering the dubious origins of the army and their eventual hand in eliminating the Jedi, taking advantage of the Uncanny Valley to highlight that there's something off about all of this seems to be a feasible thing to do.
The assassination attempt on Padme has idiocy on both sides:
Jango Fett is hired to kill Padme, but instead lends the job to a less skilled assassin.
Padme insists on sleeping by a window with the security cameras off, preferring privacy over safety even though somebody just tried to kill her in broad daylight that morning.
R2-D2 is in her room to guard her, but seems to be in "sleep" mode during then for no explained reason.
Fett's droid then tries to kill Padme by cutting open the window and deploying poisonous critters, rather than shooting a grenade in there (the lack of subtlety wouldn't matter since it's already known Padme is targeted for death). When the droid is spotted, it flees back to its owner rather than self-destructing, leading the Jedi to the assassin.
Obi-Wan, in a startling display of out-of-character behavior, leaps out of the window of a hundreds-of-feet-tall high rise to cling onto the droid without considering the possibility it could attack him while he is defenseless and hanging on for dear life. Naturally, the droid is shot out from above him, and he plummets. What if Anakin hadn't been there to catch him; what if he took too long, or was stuck in traffic? He'd be dead!
Zam escapes into a Coruscanti nightclub, but instead of using her shapeshifting to hide, she exposes herself by trying to attack Obi-Wan.
When Obi-Wan and Anakin capture Zam, instead of trying to interrogate her in a backroom at the nightclub, or simply right there at the bar, they take her outside, where either they or she could be eliminated if she had accomplices, or another droid.
Then Jango kills the caught assassin with a dart traceable to the planet he lives on, rather than an untraceable laser shot, shooting the Jedi first, or firing a dart from some planet other than Kamino to give the Jedi a false lead.
During the Battle of Geonosis, Obi-Wan and Anakin spot Dooku escaping, and Anakin orders the gunship's pilot to shoot him down, but he replies that they are out of rockets. Anakin doesn't even think to order the pilot to use the gunship's laser cannons and laser beam turrets to blast Dooku away. If they did, Dooku would've been killed off, he wouldn't have escaped, the Clone War doesn't have to happen, problem solved.
Mace Windu's first appearance on Geonosis shows him being able to sneak up on the viewer's balcony in the arena, without Dooku, the Neimoidians, or Jango Fett realizing. Instead of using this golden opportunity to capture or kill quite a few Separatist VI Ps, he wastes valuable time holding Jango at blade-point for absolutely no reason. Did he really expect Dooku to relent and halt all his plans because he thought a hired gun was in danger? Naturally, a squad of droids shows up, and Fett is able to drive him off after his attention turns to them.
Wheelchair Woobie: Cliegg Lars was confined to a hovering chair after losing his leg during his search for his wife.