Metroid: Other M may seem like an arbitrary subtitle until you notice as an acronym it reads "MOM". Also if you place the M before Other, it reads "Mother", representing Samus' relationship with the Baby Metroid and Madeline Bergman's relationship with MB.
"Other M" could also mean "Other Mother", referring to MB being basically another Mother Brain.
Or it could mean "Other Madeline", referring to MB stealing Madeline Bergman's identity.
It could also mean "Other Metroids", referring to the batch of Metroids recreated in Sector Zero. This could also be a callback to the badly-translated ending of Metroid 1 on the NES, where it says: "But, it may be invaded by the other Metroid."
If we really wanna stretch this, it could mean "Other Malkovich" referring to Adam and Ian. Ehh...?
There are people who take issue with Samus' calm and blase attitude as she narrates the story in Other M. But think about it for a few seconds, for pete's sake. She's telling a story in retrospect at an unspecified time and place, most likely where she can remain calm. In fact, she might actually be telling someone else about this, tying in with Fusion's ending. She could even be writing it down. Would she gain anything by sounding frantic or worried?
She's definitely telling the story to somebody, or narrating a journal entry. She doesn't sound frantic or worried because it's already in the past to her - she knows how it ends.
Another thing to note is why she seemed more emotionally vulnerable. She's barely had any rest at all between Metroid II, Super Metroid, and Other M. She just lost her "child" and her home of Zebes all in one fell swoop. She's been through hell and back and, like a Determinator, she kept going when she would've benefited from taking time to get proper rest.
Something very easy to miss on your first playthrough is the odd screaming that attracts monsters to attack Samus in multiple locations throughout the Biosphere, such as the first encounter with the Griptians and later with the Kihunter hive. That was Little Birdie (a.k.a. baby Ridley) trying to get you killed, and you may not have even noticed it.
Samus' reaction to seeing Ridley seems incredibly out of character, until you realize that Ridley had never truly truly died, as in Killed Off for Real, until Super Metroid. It's not that she's scared of Ridley, it's that she's freaking out because he's supposed to be dead.
Alternatively, Ridley's previous deaths took place between large spans of time - for example, there's supposedly two years between Zero Mission and Prime, and there's at least six months between Prime and Corruption, giving Samus plenty of time to process the events and understand Ridley could make a gradual comeback. She also had every reason to think he was gone for good, since his remains were consumed in the explosion of an entire planet, not to mention he shouldn't have been able to be revived by his subordinates since they all died too. However, Other M happens mere weeks after Super. He's not only supposed to be dead, but he came back in record time!
One also has to consider several other factors in this reaction as well. Ridley is Samus's mortal enemy as the one who ultimately is the cause of her parents' deaths. Also, Samus herself is still experiencing a period of deep mourning over the Baby Metroid and her failure to keep it safe. Samus has likely been carrying old wounds for a long time already given her early life, it makes a bit more sense that she's freaking out and freezing up when emotions overwhelm her senses for a moment.
This makes more sense too if you look back to Corruption, back on Norion. When Ridley ambushed her inside, Samus didn't get out of the way but stood there and shot at him as he swooped down, even though she knew it wasn't going to do much. Even after the events from the manga, she still has a little bit of fear left over. Fear is never truly gone, after all.
It makes even more sense when you consider that the writers for Other M didn't really consider the events of the Prime Trilogy when making it. If you ignore Prime and Corruption, then Ridley has only officially died once (Super Metroid) and that was supposed to be Dead for Real. So his resurrection would have looked impossible to her - she saw his body disintegrate in front of her, and how he's attacking? He'd have to be some sort of demon. She also probably didn't figure out the whole "fluffy bird thing = furry lizard = Ridley" thing either, since she looked at the shed skins of them with mild confusion, but no sort of worry.
Late in the game, Samus comes across a broken bridge that she has no means of crossing at the time without Adam's authorization. She has just lost contact with Adam, but the Deleter is getting away. So what does she do? Rather than wait around, she activates a few abilities... the ScrewAttack and Space Jump. -Matic
"Any objections, Adam?"
We don't know much about Ridley's experience with Metroids, but he sure got a lot of his energy sucked away by the Metroid larva during the climax of Samus Returns. That couldn't have been a pleasant experience, and might've left him with some fear for the little monsters. Now imagine how he'd feel facing down the fully-grown Queen Metroid in Room MW - it makes sense that he'd just cower in fear and screech like a cornered animal rather than fight back.
That's assuming this Ridley clone has the same memories as the original Ridley, which is a widespread theory. However, let's look at it the other way: what if this was a completely new being? This Ridley clone could only have been alive for what, a month at most? By examining the original Ridley's life, we can tell that his species has very long lifespans, since he was an adult during Samus' childhood and has been that way for as long it took for Samus to grow up. So the Ridley clone in Other M is basically a child, having just recently matured from its Little Birdie and Mystery Creature forms and having been in the world for only a handful of weeks. That completely re-contextualizes all of his actions in this game! He's a child with a razor-sharp intelligence and predatory reflexes, possibly targeting Samus due to some sort of genetically-inherited instinct. Can you imagine his confusion at fighting Federation marines and being attacked by the Queen Metroid?
Ever wonder how Nightmare and Ridley end up on the Biologic Space Labs in Fusion? Enter the rooms those two bosses' remains were left in during Other M's postgame portion and you'll find they're missing. The GF clearly picked them up and moved them elsewhere for further research, deeming them too important to leave behind.
Also, ever wonder why Ridley's body collapses so easily in Metroid Fusion when you encounter it in the freezer? That's not the sort of thing you usually see frozen corpses do. Unless, of course, that frozen corpse was drained of all its energy by a Queen Metroid and turned into a dry, gray husk.
At first, Adam's decision to shoot Samus in the back with a Freeze Gun seemed inexplicably cruel - many have even likened it to abuse and wondered why Adam didn't shoot the Metroid larva instead. However, the Metroid was acting calmly until after Adam already shot Samus so he might have thought that the larva wouldn't have attacked if left alone and, as far as he knew, Samus was about to provoke it. Granted, in retrospect, it was a stupid idea but it kinda made sense in the heat of the moment.
By then, he'd overheard Samus learn of his involvement in the bioweapons program, so the real reason Adam shot her as opposed to talking to her is that there was a risk she wouldn't have trusted him enough to listen at that point. That's the whole core of Samus and Adam's relationship in this game - they're both trying to learn to trust each other again.
Adam is also aware that Samus has developed a soft spot for Metroids, since he's probably heard she spared the final one in Metroid II. He didn't trust the Metroid larva to be as naive as the Baby, but decided to stop Samus instead of risking provoking the Metroid and putting her in danger.
Played from Adam's side, Samus' presence and overall participation and involvement is suspicious and possibly dangerous. Moreso when factoring in rumors of a possible assassin in his own ranks (that he observes over her comms but her presence like that could be a performance). This more than anything may explain his often overly-stiff and reactionary attitude; though his trust and belief in her comes through in the end.
Take a look at MB's hairclip. Remind you of anything? It looks like the red nuclei in the core of a Metroid.
MB also bears a striking resemblance to Samus. This may be because the Federation wanted to replicate Samus' relationship with the Baby as closely as possible, and therefore used her appearance as a base. Analytically, it also drives home the comparison between Samus and MB; she is every unhealthy aspect of Samus' immaturity given form, and her demise is due to her inability to come to terms with her own naivety, lashing out against the Federation instead of trying to maturely work through her problems with Madeline.
Madeline has her own imagery too - she has a fluffy red head of hair, somewhat reminiscent of Mother Brain's bulbous red brain.
For a while, some could think that MB is just the initials for Mother Brain, which wouldn't have been a surprise given all the other Zebes aliens onboard. We are also lead to think that MB and Madeline Bergman are in fact one and the same person, but it's a Red Herring: MB is the real name of Melissa Bergman, a different person completely.
Phantoon is the extra final boss. Anyone remember what area he was the boss of in Super Metroid? The Ghost Ship. At the end of the game, Samus is all alone on the BOTTLE SHIP, making it another ghost ship.
The Deleter subplot is almost completely dropped and left for the player to figure out themselves. Although the Japanese version's guide outright confirms that it was James Pierce, we can still piece together evidence of the Deleter's identity given throughout the game:
In some cutscenes with the Deleter we can see that the 07 on his helmet is faded, just like James' helmet.
James was the first to arrive at the Exam Center and Samus finds him fiddling with something under a computer desk after traversing multiple locked doors (possible that he locked them behind himself, but that would've been a huge give-away so who knows). He awkwardly approaches her, but is saved from her questioning when the rest of the platoon (minus Lyle) shows up. Maurice then analyzes the computer and finds that the CPU "self-destructed", which is likely what James was up to.
It's also possible that James was trying to hack the computer and failed, resulting in the CPU self-destructing as a defense mechanism.
Another possibility is that he wasn't touching the computer, but rather placing charges stolen from Lyle's body so that he could demolish the Exam Center and all the evidence therin.
Interestingly, James also asks the platoon about Lyle's whereabouts before any of them have revealed their faces. It's possible that he was well-acquainted enough with their armors and figures to notice Lyle was missing, but it's also likely that he already knew Lyle was missing and wanted to be the first to bring attention to it.
James' body is found in the Bioweapon Research Center, which is where MB was hiding. It's unclear who did him in and how, since his body is fairly intact. However, the Japanese guide confirmed that he was targeting MB, unaware of her true identity, and she somehow killed him.
James was designated the communications specialist for the 07th Platoon... but the communication on the BOTTLE SHIP is absolutely terrible and the marines can hardly contact each other. It's likely James was jamming signals on purpose in order to keep them separated and unable to rat him out.
Some retroactive Fridge with Fusion. Why would the Federation still save Samus' life from the X after she exposed their illegal bioweapons program in Other M? Well, allowing the galaxy's greatest, most famous hero to die would make them look even worse.
So why is Samus still willing to work with the Federation in Fusion anyways? Well in Other M it becomes pretty clear that the pro-bioweapons part of the Federation is not the entire organization, and that there are plenty of reasonable anti-bioweapon staff such as Adam who Samus can trust. At least, that's what she thought... until she has to blow up the BSL station too and make even more enemies.
From their exploration of planet SR388, she may have been there to see to it that their findings didn't end up in the wrong hands. Afterwards, she investigated the BSL station because the last time this happened a rouge A.I. almost wiped out galactic civilization, so Samus knew too much was at stake to let any trust issues get in the way.
Other M also explains how the Federation had cells from the infant Metroid in Fusion. Before, one would assume they acquired it at the start of Super, which doesn't make much sense given Ridley abducted it and destroyed the facility almost immediately after Samus turned the infant over. The cells used in Fusion where those they got off Samus' armor for their bioweapons program. Samus likely never brought this up because they just saved her life and faced more pressing matters.
Fitting in with Other M's "motherhood" theme, I realised the name of the space station, the Bottle Ship, is a blatant reference to a baby's bottle, shape and all. Coupled with the fact that the distress signal sent from the station is called "Baby's Cry" it does its job hammering the theme in one way or another. I do know it also may reference the age old "impossible bottle" relic but considering the rest of the game, it makes sense.
Adam locks the doors behind you to keep you on the linear path. Due to a Game-Breaking Bug, however, one of the doors in the Pyrosphere can become locked at an incorrect time, making progress impossible. Or in other words, Adam locks you in the Pyrosphere with no way out For the Evulz.
Did Adam die quickly and painlessly in Sector Zero's self-destruction? Or did he suffer an incredibly painful and horrific death having the life sucked out of him by innumerable ice-proof Metroids? This is left up to the player's imagination.