Here is a stupid involved one I came up with a while ago that borders on fan fiction:
The Samus in Other M is not the real Samus, but a clone created to be an obedient super soldier to the GF.
We know from Fusion that the GF is willing to go to great and questionable lengths to create powerful weapons, from Metroid breeding programs to attempting to capture a SA-X alive. We also know they are capable of cloning an entire organism from only cell samples and they are able to download the consciousness of an individual.
So this is how it went down. Shortly after Super Metroid, Samus goes in to a GF medical facility for a post mission checkup. Somehow the GF finds a way to copy her consciousness at that time. It would not be hard, she likely would be looking for a place to rest and let down her guard after such a grueling experience, and at this time she still very much trusts the GF. A cell sample from which to grow the clone was also collected at this time.
But they didn't just want another Samus. They wanted a better Samus, one without the rebellious nature and streak of independence that led to Samus leaving the military and becoming a bounty hunter. They wanted a Samus they could control, so they messed with the personality, building in a fail safe were this Samus will unconsciously and unquestionably obey orders given by GF officers and an obsession with pleasing them.
But the process of re uploading the consciousness into a new body failed in a subtle way - the experiences were transferred, but the essential essence did not. As a result, clone Samus knows everything that the old Samus knew but the infant mind has no contextual space in which to place the memories. The information is present, but the maturity to deal with it was lost.
This explains the out of character behavior of Other M Samus - She bows to authority without question (and is even, in her own words, exhilarated to do so,) she desperately wants to please Adam, her personality seems extremely flat, and she is completely obsessed with the last major experience Samus had before the consciousness copy was made. It also perfectly explains the more bizarre things Samus does in Other M, such as the break down when she sees Ridley.
For the real Samus this would be the 7th time or so she has confronted the beast, it really should not have been a problem. But for clone Samus, her infant mind is dealing with coming face to face with the monster that murdered her parents for the first time AND she has to deal with all the horrible memories of pain and fear from every confrontation Samus has ever had with the pirate. And all of these memories rush to the forefront of her mind all at once without any warning. No wonder she broke down.
This also reconciles the reprehensible way Adam treats Samus in Other M with her adoration of him in Fusion. Adam, for his part, hates the idea of cloning Samus, seeing it as a gross violation of the rights of someone he holds dear. But the GF is at war with an enemy that seems intent on the total subjugation or annihilation of the human species, a war they seem to be losing. And Samus alone has managed to turn the tide of the war in one small area of the galaxy. Adam is willing to do this horrible thing for the greater good. He is willing to sacrifice his personal morality if it means the survival of his people. But when it comes time to field test their creation aboard the bottle ship he is barely able to contain his disgust and guilt over his part in creating that thing before him that thinks it is Samus.
These two things also explain the varia suit incident. Due to his distrust of the clone, Adam had given orders that Samus was not to use any of her power suit equipment without his express permission. The conditioning of clone Samus made her take those orders at face value. Adam told her to go to a super heated area of the ship, so she went there. But Adam didn't tell her to use the Varia suit, so that option was subconsciously eliminated before her conscious mind even considered it. Adam, who was only monitoring the situation via audio, took some time to realize what was happening and to finally give the express order to use the Varia suit.
Finally, this explains why the game opens with Samus being revived from some sort of unconsciousness in a medical facility. At the end of Super Metroid Samus was not injured in any way. Nothing more than a physical should have been required. There is no reason she should be unconscious in an examination/quarantine room at that time, and it makes no sense at all that Samus was so disoriented and confused about where she was and the timeline of the immediate past. But it does makes sense if those were actually the first conscious moments of the Samus clone.
Also, why did she give a mission report of the events of Super Metroid? She was not on a GF sanctioned mission during Super Metroid, she had no mission to report on. And if she was giving the report as a matter of courtesy it should have included a long drawn out recounting of the events leading up to her attack on Zebes in Super Metroid. How could a single sentence be sufficient? The reason is that the council already knows what happened in Super Metroid. They got that from the real Samus. What is actually going on here is clone Samus acting out her personality programming. After a mission is completed she is compelled to give a report, and because of the timing of the cloning she believes the report has not yet been made.
Incidentally, the power suit clone Samus uses was obtained by a GF science team, but they have had little success adapting it for human use. Samus, with her Chozo DNA, is the only human that can effectively use the weapon. This is why the power suit is subtly different from previous iterations. For example, this power suit has all the main functionality of a power suit but few of the modular upgrades the actual Samus has collected. It also has some subtle aesthetic differences. This is why they need Samus clones so badly, only Samus can effectively use scavenged Chozo tech.
