I'm hardly a Metroid lore expert, but I'm generally of a mind that Clone!Samus and OG!Samus could both active at the same time -- they might possibly meet (I sense a very strained "budding into a twin sister relationship" plot on that horizon) as the Clone seeks to find out what it means to be Samus Aran and eventually settles on being someone new. I think everything currently canonical remains so, but the Clone doesn't have perfect memories because [insert plot reason here]. So she remembers things, but certain memories don't line up right, or they don't match up with what actually happened because they've been edited to make her more pliable. So some memories might come across as Deja Vu, others feel like she's watching a video of someone else's life with events and actions not belonging to her, etc. Basically the ultimate in cognitive dissonance. In that way, Nintendo could keep an ability to retcon their own retcons if they wanted by pulling an "unreliable narrator" for literally anything. Frankly, it could wind up being basically the general plot of The Third Birthday, but actually intelligible and GOOD this time around (seriously what the fuck was that game's problem?!).
As for the why she was cloned in the first place, who WOULDN'T want an army of perfectly malleable and loyal superwomen based on the template of one of the finest fighters the Galaxy has ever known? It's like questioning why the Kaminoans in Star Wars tapped Jango Fett to be the template of the Clone Army, or why the Patriots wanted to clone Big Boss in the 1970's -- the simple answer is that Samus Aran is the best at what she does, and for some reason, the government decided that the deciding factor in that badassery was genetic. Solution? Make as many copies of that genome as possible, but make genetic and psychological edits to snip out Samus' "less desireable" tendencies. Clone!Samus would probably be a prototype for that process, which based on her general levels of badassery by the end of Other M would seem to indicate the experiment was more or less entirely successful depending on what exactly they were looking for. After that, you roll out the mass production models, fit them with a reverse engineered and downgraded version (for budget reasons) of the Chozo power armor, and watch as your new army of Venom Snake: Intergalactic Amazon Brigade Edition steamrolls the galaxy.
So now the question becomes: how fucking Metal Gear Solid is this plot going to become? How much of Other M was staged to cause Clone!Samus to develop along the desired path? Some? All? None? Did she even fight an actual Ridley at all? Was it a construct meant to challenge her? Depending on federal resources, meticulousness, and callousness, it COULD be all. Every asset killed in the game was probably deemed "expendable" by higher ups no matter what, so that's a short jump to make. The real issue that needs answering is "was any of Other M even real at all, or a massive and fatal version of the Truman Show?"
If they go with the latter, I would give ALL THE PROPS to having the ringleader be voiced by Ed Harris.