This blog post contains spoilers for Metroid: Other M, and the Metroid series in general.  Do not read if you do not want to be spoiled.
 
In 2002, Retro Studios released Metroid Prime, the first 3D Metroid game, for the Gamecube.  Metroid Prime was a huge revolution; the Texas-based developer proved they knew how to make games, successfully turning a popular 2D game into an immersive 3D environment, all from a first-person perspective.  Metroid Prime remains one of my favorite games of all time, due to it being the first game to make me feel as though I was part of a living, breathing environment in a game.  Additionally, I have a soft spot for Metroid Prime 3; in my opinion, MP3 utilizes the Wii's motion controls better than any other game on the platform. 
 
However, let's go back to 2001, and pretend that Metroid Prime never happened.  Instead, give us Metroid: Other M.  The entire time I played through the game, it felt less like "another entry in the series", and more like a complete reinterpretation of how Metroid could be played in 3D.  In some aspects, Other M feels like a 3D remake of Super Metroid, which isn't that surprising.  After all, the game takes place immediately after Super Metroid, and Samus retains all the abilities she had at the end of that game.  While Retro Studios took a look at the Metroid series and tinkered with the mechanics until it worked from a first-person perspective, Team Ninja set out to keep all of Super Metroid's game mechanics intact in a 3D environment.  If you keep that in mind, it could explain parts of the game's unusual control system; holding up on the D-Pad to activate the Speed Booster is probably a lot easier than trying to keep steady using a joystick.  Hell, if the basic Wii Remote had more buttons, it's entirely possible Team Ninja would have scrapped the first-person missile sections all together. 
 
The more you look at Other M, the more it becomes clear that Team Ninja wanted nothing to do with the Metroid Prime series.  There are countless nods to the 2D games (Metroid: Zero Mission, Metroid II, Super Metroid, Metroid Fusion), but not a single game mechanic or lore from Metroid Prime remains.  Several bosses are ones Samus has fought before, only in 3 dimensions now.  The "scan" function from Prime is gone, and now Samus only scans when it's plot-relevant.  However, the biggest departure is in Samus's personality.  Samus barely says anything in Zero Mission, II, and Super Metroid; though she's rather talkative in Fusion (though that's only to an AI computer).  Fusion was released alongside Prime, so I'm not sure that makes a difference concerning Prime's development, but this is where it gets interesting.  Older games in general did not tell the stories that games tell today; Samus didn't talk because she had no reason to.  Is it because she's just a calm soldier who doesn't let her emotions get in the way, or would she be much more willing to open up if there was someone to talk to? 
 
In the Metroid Prime series, Samus is merely silent.  She had no reason to talk in Metroid Prime, but she encounters an entire race who needs her help in Metroid Prime 2, and is working alongside countless soldiers in Metroid Prime 3.  In both games, she doesn't say a word.  After the events of MP2 have concluded, Samus departs with a wave of her hand to say "See ya."  To her, saving the universe is just another day's work.  In the intro to MP3, Samus is nearly a celebrity; she's well-known for her adventures across the galaxy, but Samus isn't one to brag; she just follows orders.  Even after falling down a long shaft struggling with her nemesis Ridley, Samus isn't shaken at all; she's fought Ridley plenty of times, and isn't particularly surprised that he's there.  At the end, Samus does reflect on her adventures a bit, having killed three of her corrupted friends; it's really the only time we see her display emotion since she's wearing her helmet all the time, but after three hard adventures, it's understandable.  Samus is just that much of a badass. 
 
But Team Ninja saw that personality for Samus, and thought it really didn't suit her.  The baby Metroid who sacrificed itself for her at the end of Super Metroid weighs on her soul, and it's the only time that Samus has felt like a mother.  Those lingering feelings carry over into Other M, where Samus is self-doubting, and still shaken over what's happened.  Being reunited with her old mentor, Samus feels like she has to show responsibility, and prove that she's still capable of following orders.  This huge personality shift has left many gamers feeling bitter over Other M; it's a direct contradiction of the personality Samus displays in the Prime games, and especially comes to a halt when Ridley shows up.  Canonically, this is the fifth time Samus has fought Ridley, yet when he appears, Samus breaks down, feeling scared and lonely, screaming when he grabs her.  She still disposes of him in the usual manner (missiles), but that scene was a huge shock to many gamers.  Why would Samus feel so afraid of a foe she's dispatched so many times?  Well, once again, if you ignore Metroid Prime, this is only her third time fighting him.  His abduction of the baby Metroid in SM shows that he has his own agenda, while in Metroid Prime he gives the impression that he has something to prove; he has cybernetic implants to improve his capabilities, seemingly all to show that he's capable of taking down Samus.  In Prime, Samus and Ridley are arch-enemies, while in Other M, it's more the idea that their paths often tangle, so it's possible Ridley was just as confused about Samus being there as she was about him.  Just speculation.
 
Ultimately, Other M is less of a sequel to the franchise, and more of a reinterpretation of the game mechanics and the characters.  It's not a completely successful experiment (it features some bafflingly bad design features, such as the forced perspective pixel-hunting, and occasionally misleading directions), but it's an interesting game from a narrative point of view.  You can argue all you want over whether the story is any good, or if Samus needs a better voice actor, or whether it would have controlled better with a joystick, but despite all of those flaws, I feel the game is at least worth experiencing.