In The Phantom Menace, a lot of people complained about the submarine having force-field windows. But it's a Gungan submarine. Gungans are amphibious, so for them those windows are a safety feature.
At first, the Jedi Council is dead set against training Anakin, because he is too old, and there are all those Mommy issues... Then, in the end, the Council agrees, though Yoda still is against it. It seems like they agreed because it was Qui-Gon's last wish and they maybe felt that they owed him or something. But that wasn't the reason. At least, it wasn't the only reason. Anakin is the Chosen One (the Council never really doubted that after testing him) who is supposed to bring balance to the Force. That means eradicate the Sith. First, when Qui-Gon tells them about his encounter with Darth Maul on Tatooine and that he thinks Maul is a Sith, Mace Windu is incredulous. The Sith died out, he thinks. Without Sith, they don't need a Chosen One who is a potential loose cannon. But, when Yoda states the Council's decision in the end, he also explains that Darth Maul was indeed a Sith, they are sure of that now. And that is why the Council changed their minds. And, since there will be a second Sith, they will actually need The Chosen One. So he must be trained. It had nothing to do with Qui-Gon dying, but with realizing there actually was a Phantom Menace out there and they could not do without Anakin.
The title The Phantom Menace. It refers not only to the Sith, who are returning unbeknownst to the Jedi, and also to Anakin. Anakin is, or will be, a great threat to the Jedi, but nobody knows it yet.
Darth Maul's double-bladed lightsaber is Awesome, yet Impractical. However, Jedi don't typically swing the lightsaber as one would use a sword. Against soldiers and droids, they seem to swing with little effort. Yet, against another Jedi or Sith, they fall into practical sword fighting and add a great deal of force. Because a lightsaber cuts so easily, the only other weapon that could pose a legitimate threat and pose a fight is another lightsaber. Back to Darth Maul, it's not so much as a double-bladed lightsaber from this standpoint. It's more of a lightsaber staff. His moves are clearly inspired by bo-staff fighting.
There didn't seem to be much reason behind the battle of Naboo (aside from providing action sequences) at first. Once the movies are seen in order, it is much easier to see the subtleties of the ultimate plot and how Palpatine really was manipulating everything from the very start. The Phantom Menace was really a Xanatos Gambit by Palpatine. No matter what happens, he wins. If the Trade Federation successfully invades and takes control of Naboo, he has the necessary sympathy vote to become Supreme Chancellor. If the Queen makes it to Coruscant to plead her case before the Senate, the accusations get that much more dramatic, the Trade Federation's allies have to step in more bluntly to spin the damage, and Palpatine gets a larger sympathy vote. If the Queen returns to Naboo and overcomes the droid army, Palpatine gets sympathy and badass vote. If the Queen returns to Naboo and gets captured by the Trade Federation, he still gets his sympathy vote. Nothing at all the heroes could have done could have changed the outcome to anything but a favorable one for Palpatine. The only thing that could even theoretically have hurt Palpatine is the Jedi capturing Maul and have him testify in a senate hearing as to who his master/employer is.
The Gungans celebrating their victory after the droids holding them at gunpoint suddenly go dead might seem a little silly, considering that technically, they'd just lost their battle against those droids. However, winning the battle was never their objective in the first place: as they discussed with Queen Amidala, their purpose in marching out on that field was to draw the vast majority of the droid army out of the city and keep it busy while her military and palace guard went after the droid control ship and the viceroy in command of the invasion respectively. By holding the droids back as long as they did and then retreating as necessary, they achieved their real objective, which was to win the war. Their celebration and subsequent acclaim at the parade held in their honor is well-earned, since Amidala and her people couldn't have retaken the planet without the Gungans holding the line.
If nothing else, they're probably celebrating also because now the droids won't kill them.
Panaka staying with the ship on Tatooine. At first glance, this seems like an odd move given that Panaka is a level-headed military-type. And yet, that's exactly why it would be better if he stays behind. Tatooine is a haven for criminals and shady figures — people who don't want to be found. Having Panaka along would make it much more difficult to interact with the populace because his demeanor screams law enforcement, and, given that Qui-Gon's a Jedi Master, any battle skills Panaka would bring to the table wouldn't add all that much more. Instead, an innocuous fool like Jar Jar is much more handy to bring along and this also prevents him from messing with the already damaged ship or accidentally sending a transmission (and thus alerting the Trade Federation of their location.)
Jake Lloyd's Anakin seems too sweet and too nice with no flaws to be a believable character, much less the origin of Vader. However, there is a lot to this kid. His building a droid is significant. Why? Because he stole the parts. And, bear in mind, Watto's not that bad a slave owner. He treats them respectfully, lets Anakin go home early, and lets Shmi stay at home and not work in the shop. So the that Anakin would still want to steal from the guy who, for all intents and purposes, is the only father-figure he has, is telling of his lack of respect for authority, which will became vitally important in leading to his hush-hush relationship/marriage, which will become incredibly important as it drives a wedge between him and all his friends except Palpatine.
On closer observation, he's also shown to be reckless (utilizing a ramp to get ahead in the race, getting involved in the space battle), aggressively confrontational (with Sebulba), manipulative (watch how he convinces his mother to let him pod race by discussing her own lessons about helping people), defiant (to the supremely powerful Jedi Council, no less!), and arrogant (he has no problem talking up his piloting and engineering skills). These qualities seem innocuous in a child, but they wind up being major character flaws for him as an adult.
YMMV on how the viewer feels about Watto, too. At the end of the day, he's still a slave owner actively exploiting a nine year old child as free labor. His slaves are fitted with chips that will explode if they ever try to escape. Shmi finds Anakin's involvement in the pod races terrifying and dangerous, but she has no power to object to Watto using him as a contestant for gambling purposes. The entire reason why Anakin's freed stems from Watto's willingness to literally gamble their lives away. Later in Attack of the Clones, he refers to selling Shmi as "business." Suggesting that slave owner was Anakin's first paternal model holds more disturbing implications than not and may actually lend some insight into the dynamic between Palpatine and Vader.
If you take the time to consider him, Jar Jar may be one of the most selfless and kind-hearted characters in the entire saga. He's saved by Qui-gon, and although he could have merely thanked him and left, Jar Jar informed him that he was honor-bound (despite being banished from his own society and no longer influenced by societal influences) to give Qui-gon a life-debt of service. He then leads Qui-gon and Obi-wan to the Gungan city, despite knowing he'll face capital punishment for returning, and even THANKS Qui-gon for saving his life before Boss Nass enacts capital punishment with glee instead of begging Qui-gon to take him with him away from his fate (and it's because of him helping Qui-gon that he had returned to the Gungan city in the first place). He's then seen going with Qui-gon into Mos Espa, despite not being asked to aid Qui-gon and is often seen trying to help Anakin with his podracer. And when he's both on the ship with Padme and sharing a private moment with the Queen, Jar Jar connects on an emotional level concerning the personal toll of their journey and the affects of the war on ALL of the species on Naboo, and not just speaking from a removed ethical point-of-view or political angle as so many of the other characters are when talking with the Queen. It's important to also note that Jar Jar, true to his word, finally leaves Qui-gon after he dies at the hand of Darth Maul. He may be a bit too buffoonish in a number of scenes (like the battle towards the end), but it's clear to see that he was someone who constantly tried helping where he could, even if he messed up in the process. Not to mention, despite being shocked he's been promoted to general, he's more than willing to go into combat with his fellow Gungans.
The parade music at the end of the film is a jumpy enthusiastic tune in a major chord sung by what sounds like a children's choir. Put it in a minor chord, slow it way down, and replace the kids with a choir of depressed old men, and you get the Emperor's theme in Return of the Jedi. Consider that Palpatine (featured in the Parade sequence) and the Emperor are one and the same, and you begin to wonder how old and in what emotional state the kids in Phantom Menace would be at the time of the Battle of Endor...
"The Queen demands you take her handmaiden with you". Why would Padme risk leaving the safety of the ship to see what Tatooine is like? Because the Jedi Master is going, and he's the best protection for her, especially if the Trade Federation were to trace the ship's location. Better to get the real Queen as far away as possible.
Why would a planet elect a 14 year old Queen? The position is considered sacred, above politics and pure. Best suited for an innocent child.
There are a lot of criticisms towards Jar Jar's character design as a whole, among them being the way the Gungans speak. But one must keep in mind that the Gungans were the native populace of Naboo, and the Galactic Basic would be a new language to them. Their way of speaking is because the Basic was combined with their original Gungan language.
Why does Anakin have an American accent when his mother has a Swedish one and the other person he's always around, Watto, has some kind of Italian/Middle Eastern accent? It's because he listened to the pilots who came into Watto's shop and admired and wanted to be like them. Most of the human ones likely were Corellian (like Han) and have American accents.
The way Qui-Gon and Darth Maul act during their duel while being separated by an energy gate is a summation of the Jedi and Sith philosophies. Qui-Gon closes his eyes, meditates and focuses on summoning the best of his training to improve his skills. Darth Maul paces around, gathering anger and gaining a tunnel vision on his enemy he constantly glares at, focusing on his weak points.
A phantom is like a ghost, a specter that is physically not there... yet it stands before us in spite of that. A hologram is a virtual projector that makes a person appear before an audience as if he's really there despite the fact you cannot touch him for he lacks substances. Save for one scene, and all the scenes that featuring his secret identity, which character only appears as a hologram for the majority of the film?
A mix of Fridge Brilliance and Fridge Humor. When the decoy queen commands Padme (the true queen, mind you) to go clean R2D2, she has this goofy little grin on her face. Why? Because this is a chance to prank her boss, as it were. Padme has her hand maidens do all sorts of crap and now the decoy is able to get a little revenge. "Oh, go clean the filthy droid, Padme. He deserves our thanks, after all!" The decoy knows Padme can't complain so takes the opportunity to get in a little fun. You can actually see the other handmaidens smirking in the background.
One of the biggest complaints about The Phantom Menace is that it is so goofy and kid-friendly; one of the biggest complaints about the Prequels is they don't feel like the Original Trilogy. But that is the point. The original trilogy was a Space Opera and followed that flow. The Prequels are a Greek Tragedy, with Oedipus Rex being the main influence. Thus it doesn't follow the same ups and downs of the original because it is working from a different playbook. This also explains why The Phantom Menace is so silly: Greek Tragedies usually start with light-hearted comedy and goofy characters before evolving into dark and tragic stories. The Phantom Menace is merely the goofy 20 minute opening act of a Greek Tragedy.
If people come to this movie knowing nothing about it, they're treated to a small clue as to Padmé's true identity when she says to Qui-Gon, "You assume too much." It's a Meaningful Echo of what Nute Gunray says to Queen Amidala earlier in the film.
In the Expanded Universe, the Empire was notoriously human centric and xenophobic — which makes perfect sense when you realise that the Empire's founder, Palpatine, grew up on a planet with two different sentient species that were constantly in conflict and distrusted each other.
All the ridiculous outfits that Queen Amidala wears make more sense when you realise that they're to throw everyone in and out of universe off from the slight differences in appearance between Natalie Portman and Kiera Knightley.
The revelation that Anakin built Threepio was greeted with some derision as showing the Prequel Trilogy's over-reliance on Already Met Everyone, but if you think about it, it's actually filling a Plot Hole. See, while The Empire Strikes Back is an excellent movie, if you think about it and the rest of the Original Trilogy, there is absolutely no good reason why the Empire would have given the dismantled Threepio back to the heroes in their cell when they were prisoners in Cloud City. Threepio is a Rebel droid, after all, and the Empire could get valuable intelligence from him, such as the Rebels' codes that they use in communication. Yet Vader, the ranking Imperial present on Bespin at the time, and one who punishes failure and treason harshly, allows Threepio to be returned to the other main characters. However, Vader is shown to not be irredeemable in the end. Ultimately, the reveal that he built Threepio provides an explanation as to why Vader had the droid returned to the custody of his friends — he was feeling ever so slightly in the mood to Pet the Dog. In fact, there's a story from Star Wars Tales, which was a series devoted to telling What If? stories, called "Thank the Maker" that posits this very idea.
The Trade Federation battleships seem to be of a remarkably poor design, with the entire thing going up like a fireworks factory due to a couple of torpedoes hitting something in the hangar bay. Three things to keep in mind:
The battleship is, according to the expanded universe, based on a freighter design, making it more akin to a very powerful merchant cruiser or privateer, rather than a designed-from-the-keel-up warship.
Hangars may contain all manner of volatile things (such as fuel or ammunition) which could set off a disastrous chain reaction (something not unknown in Real Life aircraft carriers).
It was very unlikely for any pilot to actually get into the hangar bay of a hostile ship. Over a timeline covering around 60-70 years, we only see such a feat accomplished four times on film, two of them involving Anakin (who would become a renowned pilot), one involving his grandson (who is himself the son of another renowned pilot), and the fourth an honorary mention by Poe Dameron (not a hangar bay, but the interior of an enemy base that someone else blew a hole in for him to get through).
Queen Amidala has a decoy so any attempts at assassination would fail. Sounds bad, but it's just something that comes with such a high political position. Then you remember that she was supposed to be fourteen in the movie, so they would have to hire a similarly aged young girl to take any and all bullets intended for the Queen.
Presumably, a little In-UniverseDawson Casting would help with that, but note also the blasters concealed in the arm of the Queen's throne, and how she and her handmaidens (and everyone else working for her) are evidently expert shots with them. How common is political assassination on Naboo, that its government would have (and regularly need) such efficient and well-practiced counter-measures?
We're also not told a lot about the exact nature of Naboo's dispute with the Trade Federation that led to this blockade and invasion in the first place, but one does have to wonder what kind of dispute could justify starting such a massive conflict. For all of its silly-sounding name and sleepy suburban appearance, Naboo clearly has more to it than meets the eye, and one suspects a militaristic regime lurks just beneath the surface of its pleasant-looking society.
Which actually leads to a bit of Fridge Brilliance, as Anakin's idealization of Naboo helps foster in his mind the idea that a ruthless, pragmatic, and militaristic government can give its citizens a good and happy life and no one will mind at all.
Padmé in particular is clearly more hard-bitten and politically experienced at fourteen than anyone gives her credit for being. Also, though her monarchy isn't hereditary, where are her parents? One would think even if they have no real political power from being related to the queen, they still ought to be there with her in her palace, but no, this fourteen-year-old is ruling alone. I don't see any parents and family for her handmaidens there either. Maybe Naboo is a Teenage Wasteland as well?
Realizing that every last character signed their proverbial death certificate in the ending. Anakin gets trained by a grieving, inexperienced Knight barely out of a Padawan braid, who is completely unable to handle the task of an unruly unconventional trainee who hasn't been confined to an enclave all his life. Obi-Wan, said grieving and inexperienced Knight, will be killed by Anakin later. Padmé; and Anakin have a Precocious Crush that will end in a tragic mess of a marriage and their mutual destruction. Palpatine has been elected Chancellor, starting his rise to power that will eventually destroy almost every other character present, directly or indirectly. Worse, it all looked like a victory at the time.
Even Palpatine sealed his fate there, given that it was Darth Vader who eventually killed him. So, there's that.
C-3PO being built by Anakin means that Luke and Leia kept what was effectively their half-brother as a slave.
Qui-Gon's funeral. They're watching a man they cared about burn. Anakin is even standing on something, to get a better view, as his first proper father figure is slowly being roasted and turned to charcoal.