Did the SA-X ignore Samus for the Omega Metroid due to sheer instinct? Or did it develop its assimilated human emotions to the point of wanting to save Samus for being such a Worthy Opponent?
Some believe that Phaaze was simply a massive parasitic lifeform, without the sentience to understand the detrimental effects of its reproductive cycle, and that Dark Samus, which was actually a Metroid Prime that assimilated Samus's Phazon suit, enslaved it.
Samus herself could be interpreted negatively. It's canon that she's driven at least partially by revenge against the Space Pirates for destroying her home, and after all the destruction she's brought down on them, may have actually succeeded in exterminating them. Though her enemies are undeniably dangerous, she's attempted genocide against the Ing, X-Parasites, Metroids, and all Phazon-based life with varying degrees of success. Her only act of compassion was in sparing the infant Metroid, which she immediately left in the hands of scientists to study. Also, Metroid Prime and the X-Parasites became a threat to the galaxy after taking on her form. Make of that what you will. Not to mention her habit of, intentionally or not, destroying planets.
Anticlimax Boss: Arguably, the Omega Metroid in Fusion; not only is it nowhere near the hardest boss in the game, it isn't even as hard as its previous appearances in Metroid II. However, it's arguable whether it counts as the final boss; most fans believe that the SA-X is the true final boss, and the Omega Metroid is just designed to be one last challenge before you escape the station.
Kraid in Super could be taken out with four well-timed super missiles before he even finished rising up from the ground. Ostensibly a glitch, Kraid can be defeated in little time even without it by a seasoned player.
And Mecha-Ridley in Zero Mission, who is incredibly easy. He gets more challenging, however, if you've gotten 100% of the items, or if you're doing a 15% item run.
Brown Note: For players, especially wearing headphones, the Power Bomb's explosion in Fusion can really hurt your ears, even on low volume.
Complete Monster: Ridley, in the manga adaptation, is the series version of evil incarnate. His first encounter with Samus has him landing on Samus' home of K2-L, and telling his minions to "First enjoy the slaughter to the fullest!" Not long after killing most of the planet's workers, he tries to kill the three-old-Samus, but her mother saves her. He later eats her parent's bodies after Rodney Aran destroys his ship and badly wounds the giant space dragon. This comes up later when Ridley uses this fact to send Samus into a Heroic BSOD.
Demonic Spiders: The Metroids themselves (though the base forms are ALOT weaker in the Prime trilogy). In the 2-D games, they inflict massive amounts of damage, and the only way to kill them is by freezing them with the ice-beam and repeatedly blasting them with missiles. While they're a lot weaker in the Prime trilogy, the Fission Metroid in the first game are this, they take a lot of damage, and then split into other Fisson Metroids that only take damage from a certain beam, which is really bad when see the ones that only take damage from the ice beam due to its low rate of fire.
Ensemble Darkhorse: Ridley has gathered a big fanbase around him (and in the manga, he was essentially the one who steals the show). Also, Rundas from Metroid Prime 3, Sylux from Metroid Prime Hunters (the appearance of a ship that looks like the Delano 7 in the 100% ending of Corruption may have been a nod to Sylux's popularity), and Anthony Higgs from Metroid: Other M.
Epileptic Trees: In Fusion, the extent to which Samus absorbs the X is only vaguely hinted at. Thus, it's unclear as to whether she's absorbing their DNA, or just their energy.
Another interpretation- Metroids absorb energy. Samus is imbued with Metroid DNA. Therefore, Samus is absorbing energy.
It's believed that the Ing are a form of semi-solidified Phazon. This is supported by the appearance of the Phaze-Ing in Prime 3, which is basically a blue Inglet. This could very well be untrue, though, as it raises a lot of other questions, (like why Phazon kills most Ing).
Almost nothing is known for certain about Sylux, except that it hates both Samus and the Federation. Fertile ground for the trees right there, including that it is female.
Nobody really knows what Kraid is or what his actual connection with the Space Pirates is, beyond being a high-ranking member, but everyone sure loves to speculate. Pre-Zero Mission, a lot of them focused on whether he grew or was enhanced between the original game and Super Metroid, because he went from being tiny to being huge.
The identity of the dead soldier lying outside Kraid's room in Super Metroid. The body's purpose is to this day unknown, and has prompted much discussion and speculation over who it was, what faction it was with, and why it was there. Theories abound among fans, with claims that it could be anyone from Expanded Universe bounty hunter Houston Armstrong to Weavel (from Prime Hunters). It doesn't help matters that the soldier is the only human-looking sprite left on Zebes.
Fandom Heresy: If you say that you liked Other M or even go as far as to say it was your favorite in the series, expect a few eyebrows to raise, and maybe a fight to break out.
Fanon Discontinuity: There is a Metroid Manga that is supposedly canon, but is ignored even by most who bothered to look it up in the first place. Not helping is that it isn't entirely consistent with the games.
Other M is often treated this way, mainly due to Samus supposedly suffering from Badass Decay according to detractors, but also for several other elements, such as the convoluted reincarnation of Ridley.
Germans Love David Hasselhoff: Much of the Japanese series' fanbase is based in America, which might be why the 3D revival of the series was given to an American development studio.
In fact, Other M was designed mostly to get the Japanese to buy it; it worked, but at the cost of losing a good part of the (much larger) American fanbase.
In Fusion, the winner goes to the species of X-infected Ki-Hunters. They're quite quick, contact damage with them takes about 50 energy, and their stinging attack takes a way a full energy tank. They're also found right before and after you have to flee from a super powerful SA-X, causing frustration for anyone who gets unlucky and isn't able to reach a save spot in time.
Good Bad Bugs: "This is an Elite Space Pirate. Elite Space Pirate Description 3."
Growing the Beard: While Metroid and Metroid II: Return of Samus were perfectly good games, Super Metroid improved absolutely everything, set the standard for all Metroidvania games in the future and is now regarded as one of the finest games in history.
It Was His Sled: When the original game first came out, many players were shocked to discover that Samus is a Girl. Not so much anymore, in large part because one of the original reasons why it was originally so shocking (a girl protagonist in a video game?!) is pretty pat nowadays.
Also, Samus suffers sudden shell shock against Ridley in Other M.
Magnum Opus: Super Metroid is almost unanimously considered one of the best, if not THE best example of Even Better Sequel in all of gaming. With stellar gameplay, memorable boss fights (including one of the most highly regarded final bosses of all time) and masterful minimalist storytelling, it regularly tops lists of the greatest SNES games ever, as well as regularly appearing on, and sometimes topping, lists of the greatest games of all time.
Magnum Opus Dissonance: Sakamoto wanted to top Super Metroid's success with Other M. As the split-opinion shows, the results were far less than stellar.
Also, Admiral Castor Dane, in part due to a scene where it seems he's standing in the Urtagian acid rain, which is strong enough to kill well-armored Samus in a few seconds, with no protectionnote The flagship above him probably acts as an umbrella, but you still have to wonder if some rain gets around it. Also, he's using a spaceship as an umbrella..
Mis-blamed: At one point, Yoshio Sakamoto gave an interview with Kotaku where he said that he initially wanted Other M to be "on-rails." What he meant by on-rails was "on a 2D sidescrolling plane." What the article gave the impression of with what he said, however, was "Rail Shooter." Unfortunately, the misinformation spread like wildfire, and fans were up in arms over how Sakamoto was trying to derail the series with an unneeded Genre Shift. The uproar dissipated once Sakamoto was able to clarify what exactly he meant.
Gunpei Yokoi has always been viewed this way. He is the series creator and all but he had help. Particularly when he was looking for ways to make the game and its sister project more distinct from each other Yoshio Sakamoto suggested adding in a maze because he felt the game was too short, which lead to maze becoming a core game play feature.
Never Live It Down: Fans like to say that any planet Samus lands on will explode at some point. They must not think Tallon IV, Alinos, Arcterra, Aether, Norion, Bryyo, Elysia, and the Pirate Homeworld exist, then.
Wall-jumping in Super Metroid, due to the unforgiving timing required to pull it off correctly. Fortunately, there is only one optional occasion where you have to use it before you acquire the Space Jump, which is a much easier way of doing the same thing. Fusion, Zero Mission, and Other M subsequently made wall jumping a lot easier. And then some difficult romhacks of Super make the timing even more unforgiving.
Any long-time Metroid player's blood pressure goes up when they see water in a Metroid game. Though this gets MUCH better once you get a certain suit upgrade.
Metroid II is underrated, overshadowed by further instalments and sadly blamed for being more linear and empty than Super Metroid. Despite this, it was the game that brought Save Stations, the space jump, the spiderball and the current design of Samus’ armor. Samus was able to shoot down and kneel for the first time which was easier to kill some ennemies. For the story, it was also the game that brought the evolutions of the metroid and introduced the “baby”.
Squick: A blink-and-you'll-miss-it example. As you are entering the Olympus, you see Ghor in containment room being scanned. During this time, you see him scratching his head. The problem? This also means that he is scratching his brain.
Tainted by the Preview: Not exactly preview, it's more like tainted from the start. According to a interview with the game director Yoshio Sakamoto, during the development of Super Metroid, it was actually close to being put down not one, not two, but three times. And one of the biggest critics of the game was actually Gunpei Yokoi — yeah, that's right, the creator of the series. Reportedly, he often angrily asked the team "Are you trying to make a goddamn masterpiece?". Well, the game came, and it was pretty much a masterpiece, and Gunpei apparently liked it so much that he for a long time used it as a reference of how a good game should be. Sadly, he and Sakamoto never had the time to make up before his unfortunate death.
That One Boss: Yakuza, Nightmare, Phantoom. And Ridley is hardly a fair fight, in any game.
That One Level: The second play through of Sector 2 TRO, in Fusion, is arguably the hardest part of the game due to the plant overgrowth, lack of weak enemies, and the fact that every enemy you do encounter deals at minimum 1 bar of energy in damage (nevermind the SA-X, who takes 3 of them every time you touch her).
Not only do we never find out what happened to the rest of the Diamont, we never even find out how Spire got separated from them in the first place.
Sylux's backstory states that it has a deep-seated hatred of the Galactic Federation, hating Samus by proxy. That's pretty much all we ever find out. Though his ship is possibly seen in The Stinger for Corruption, so there's a chance of developing this.
Super Metroid was overshadowed at the time of its release by the hype for Donkey Kong Country, people didn't start acknowledging it as one of the greatest games of all time until 1996 or so.
Metroid Fusion was originally the black sheep of the franchise, with its focus on storytelling and linearity dividing fans. Now, it's remembered more for its boss fights and interesting deviations, while Other M gets the insults.
The Woobie: A young girl is the Sole Survivor of not one, but two holocausts, the first of which happens when she's three?