* AndYouThoughtItWouldFail: Before release, Nintendo and Retro made so many controversial choices with the game that no one, not even levelheaded fans and critics, were kind to it. First off, Nintendo letting Retro, an unproven American studio, develop the game rather than doing it themselves. Second, making it in 3D which many expected but was still a controversial choice especially given [[PolygonCeiling how many franchises started to crumble with that jump the gen before it]]. Finally, making it first-person was thought to be the final nail in the coffin for the game having any hopes of being good and feeling like ''Metroid''. When it came out, not only did everyone feel like it was a true ''Metroid'' game, it and its two sequels are generally considered to be among the greatest games of all time.
** The Omega Pirate is the second-to-last boss, but it can be defeated extremely quickly with Super Missiles (it dies to three after you make it vulnerable).
** Metroid Prime itself. While the first part of the battle is quite challenging due to Prime's insanely high stamina and very prolonged length of the fight, the second phase is much easier. The strategy is reduced to dodging shockwaves (which don't even hurt that much if you have enough Energy Tanks), switching visors and waiting for Prime to drop a batch of Phazon so you can zap it with your Phazon Beam, rinse and repeat. While it now spawns Metroids to hinder you, a Power Bomb and/or the Phazon Beam makes quick work of them.
* AwesomeMusic: Kenji Yamamoto strikes again, with a mix of new tunes and remasters of older tracks. [[https://youtu.be/QQCZIb0fbt8 Case in point]].
** Chozo Ghosts. Durable, immune to everything but the Power Beam, capable of knocking out your visor with their attacks, and they spend most of the time invisible. On the bright side, the Super Missile combo works on them, and once you get the X-Ray Visor, they can be tracked when they're invisible.
** Wave Troopers. Ice Troopers can easily be killed with [[LiterallyShatteredLives a charged shot followed by a missile]], Power Troopers can be knocked around with Super Missiles, and the Plasma Beam is powerful enough to cut through Plasma Troopers. However, there's no easy way to deal with Wave Troopers; stunlocking them only works if there's one of them, the Wavebuster is AwesomeButImpractical, and regular shots are very weak. On Hard, too many Wave Troopers spawning can easily screw you over during the Omega Pirate fight.
** Fission Metroids. Basically much more powerful version of the standard Metroids, you can only damage them with a beam that corresponds to their color. They take a long time to kill, and when they take enough damage they split into more Fission Metroids, meaning you can end up fighting several at once. Sometimes you're better off running from these things than you are fighting them (or dropping a [[ThereIsNoKillLikeOverkill Power Bomb]] on them, which [[NonElemental will kill them regardless of color]]), and thankfully, you only encounter them in the Impact Crater, so they're not too hard to avoid (in ''Trilogy'', Fission Metriods can be encountered in the Phazon Mines, and they're no less annoying).
* FirstInstallmentWins: While ''Metroid Prime 2'' and ''3'' are not bad at all nor disliked, the original game is much more esteemed and acclaimed.
* HilariousInHindsight: Thardus is a rock monster whose weak point you have to use Samus' Thermal Visor to find. Meanwhile, the crew of ''Film/GalaxyQuest'' have trouble fighting a similar rock monster because they believe that it has no weak points!
* PlayTheGameSkipTheStory: Because scanning for logbook entries is completely optional, its entirely possible to get through the game with only a surface understanding of the games plot, and without learning any of the game's unraveling backstory and lore.
* SpecialEffectFailure: The updated Trilogy version on the Wii has one with the particle effects for the Arm Cannon when it's charging up. Because the Arm Cannon can be freely moved at any angle with the Wii Remote (unlike the [=GameCube=] version where the weapon had limited movement), the particle effects for charging shots became glitched during the porting process of the game. The developers couldn't figure out how to get the effects to work properly and opted to remove the effects entirely. It's very noticeable with the Ice Beam since it no longer forms ice over the Arm Cannon if the shot is being charged up.
* ThatOneBoss: Quite a few.
** Thardus. Most of the time it's throwing boulders at you or curling up and rolling around the room, where it's very hard to dodge because of its size. To damage it, you have to switch to the Thermal Visor, shoot out the highlighted boulder in its body, switch back to the normal visor, and continue blasting away at the highlighted boulder. You have to do this ''a lot''. And as the fight goes on, it summons a ''snowstorm'' that makes it impossible to see more than 10 feet away, which makes it a whole lot harder to dodge its rolling. Annoying and long enough normally, but Hard mode is a whole other beast.
** The Omega Pirate is a ''massive'' Elite Pirate found at the bottom of the Phazon Mines. For starters, the room has several pools of Phazon in it that are extremely easy to accidentally walk into when you're trying to avoid the Omega Pirate and the Beam Pirates. He's also good at backing players into corners and smacking them for ridiculous amounts of damage, and while you can stun him with Power Bombs, it's hard to get away without losing a lot of health. Even worse, he spends most of the fight with a shield up that blocks all weapons except Missiles (and the [[NotCompletelyUseless Flamethrower]]). Damaging him requires you to jump through a bunch of hoops; first, you blast off his shoulder and knee armor, then he vanishes and summons several [[DemonicSpiders Beam Troopers]]. As you fight the Troopers, you have to use the X-ray visor to see when he goes into a Phazon pool, which allows you to hit his heart and actually damage him. On Normal, this is all fairly manageable if obnoxious as the Beam Troopers are there to harass you, but he's a nightmare on Hard. Quite aside from his boosted damage and massive health bar, the Troopers that he summons become a major threat, especially the Wave Troopers. What makes this worse is he's fairly squishy with his shields down as three Super Missiles can end the fight fairly quickly but that's why the Beam Pirates are there to harass you.
** Meta Ridley. He starts out almost hilariously anticlimactic, flying around your platform and throwing bombs, missiles, and lasers at you, all of which are easy to dodge. Then, you get him down to about a fifth of his health, and his wings burn off. He lands and goes into melee mode, where he lunges at you and takes off huge amounts of health with every hit. He also gets much harder to damage, and has to be stunned with a well-timed missile before he exposes his weak spot.
* ThatOneLevel: Quite a few.
** Phazon Mines is not only a nightmare to navigate due to its multiple levels and incredible size (it's easily twice as big as the Chozo Ruins, for starters) and labyrinthine layout, it also has a bunch of DemonicSpiders lurking around. The first foray into the level, right after the Wrecked Frigate is one of the toughest sequences in the game, and the march to getting the Power Bombs can take upwards of 35 minutes to complete- with ''no save room until '''after''' you get the Power Bombs.'' You also have to march in and out of the Mines frequently, as getting the Power Bombs and Grapple Beam opens up the ability to get the X-Ray Visor and the Plasma Beam, both of which are necessary in navigating the lower portions of the mines and gaining access to the boss of the area.
** The Impact Crater is the toughest place in the game, and it reeks of being as hostile as possible- danger lurks around every corner, Metroids are abundant, navigating the place is tough and it's creepy as hell.
* UncannyValley: Samus' EyedScreen when a flare makes her face visible hasn't aged well.
* SugarWiki/VisualEffectsOfAwesome: While the games polygon count is rather average (understandable given the UsefulNotes/NintendoGameCube only had so much memory to use for such an ambitious game), Retro Studio nailed down the lighting, textures and atmospheric effects of the games environment so well, that so to this day, the games graphical presentation still holds up as first rate.