* 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.
** 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 the charged shot + missile trick, 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.