Other M is canon "to a point".

Samus doesn't remember everything that happened on the Bottle Ship. She really did have a fight with the reconstructed Mother Brain. Adam telling her not to use certain upgrades even when the situation called for it was all a lie: she lost them the way she usually does, and had to regain them in the usual way.

Is this some developer's statement, or just your personal wish list?

Er... dude... it's a wild mass guess. As in, you know, making shit up?

Sakamoto has said that Samus doesn't lose her equipment.

Metroid Other M was supposed to be a Fusion sequel involving a Samus clone combating a Metroid/X Parasite/Space Pirate invasion of planet Earth. This explains the Metroid Queen, the mother brain, and the rehashes content in general. However, because the entire team of developers was made of old timey 2D programers the project languished in development hell for years.

Eventually, Iwata stormed into Sakamoto san's office, slammed his fist down on the desk and said "We are announcing a new Metroid at the Electronic Entertainment Expo so finish the game, dammit!" "With all due respect, supreme commander Iwata, you said the reason gaijin where making prequels was so we could have devote the proper time to sequels. There is still so much of their work I have yet to see honestly and the trilogy bundle should hold the fanbase over till next year's E3." "You want another year when I gave you nine? Whatever you have done, something will be at this E3 and released within the year, and it will be on your head if it fails!"

Desperate, Yoshio Sakamoto turned to Team Ninja, who were able to salvage something that resembled a game out of the development hell but much padding had to be done to meet the announced release deadline, which they decided to do with cutscenes since they work with a company that does nothing but make pre-rendered CGI clips anyway. The gameplay did not just suffer from the rush job but multiple sections of the script were cut out or altered, leaving the narrative without a clear focus and several stillborn plot lines. In particular, the scenes of cities and military combat were going to be actual gameplay but were recycled into cinematics.

This was not a clone but the actual Samus, yet her suit looked and behaved much differently than we remembered and she was a lot more awkward than we remember and seemed to have some kind of amnesia or mental disorder never before hinted at, as if she was someone else. The Metroid Queen was pasted over a completely different creature, explaining the wide discrepancies between its Metroid 2 fight, due to time constraints. MB's invasion is artifact from the original script and the emergency break was just a quick handwave from overworked writers.

Thus Other M became to video games what Alien 3 and Alien Resurrection are to film and just as Joss Whedon refuses to take responsibility for those films so too does Team Ninja for the game, with the honorable company man Sakamoto san taking all the heat.