It's wild you say this. I was thinking of exactly that last night, lol.
The Prime games officially becoming their own, divergent timeline, I mean. In some sense, I'd understand if they went that route, especially considering it would free them from the creative shackles of all these stories eventually having to lead into the events of Metroid 2.
I think one of the wilder, more out there mindfucks they could potentially pull out of their back pockets is if somehow, the planetary impact caused by one of the Leviathans from Phaaze already split the timeline prior to the events of Prime 1, and we've been playing as a Samus on a different path, the whole time. Aether's Leviathan famously split the planet into two parallel dimensions (which is weirdly paranormal for Metroid, even despite the ghosts in Super and Prime 1), so the foreshadowing for such a revelation will have already been present.
On the other hand, an aspect of Metroid I really appreciate is how straightforward its storyline has historically been. It's the polar opposite of Zelda, in that regard, as there's never been any convoluted timeline hijinks complicating matters more than necessary.
I think if the games ultimately remained in the same position of leading into Metroid 2, that certainly wouldn't be the worst thing. The Prime subseries is interesting from a narrative standpoint, because it recontextualizes Samus's mission to SR388. It wasn't just what the Pirates did on Zebes that immediately lead to the Federation seeking to eradicate an entire species, but rather, a series of compounding incidents, and various crises, that inevitably lead to that point. It makes it so that killing the Metroids on their homeworld was a last resort. I think that'd be in line with what we know of Samus's character. Personally, I think she'd only do something like that if she knew it was the only option left.
Yeah, it wouldn't be the worst thing. But like you said, I do think that at some point, Tanabe and Retro are going to desire a bit more in the way of narrative freedom. Especially since, as of yet, it's always been a bit of an uneven yolk when it comes to how the Prime games are beholden to the main series' timeline as far as their placement, but Sakamoto and co. can opt to barely acknowledge the events of the Prime line. To the point that even
Ridley's surprise appearance at the end of Samus Returns came off more to me as saying "Alright, those games DID happen, happy? Moving on!"
The other thing, and I've touched on this briefly before, is that some organizations, especially the Space Pirates, themselves, come off quite differently in the Prime games, compared to how they're portrayed in the main series. In the main series (and the Zero Mission manga), they come off as a cabal that was more a grand nuisance to the Federation that was raiding ships and colonies (granted, they still ruined Samus's life when they upended her peaceful childhood!). That's why Mother Brain asserting control, assuming leadership and giving them a base of operations on Zebes was a big deal, because now we had an organized outfit, which then proceeded to make things significantly WORSE once she directed them to steal the Metroids that the Federation had acquired from SR388. They had officially graduated to something that could threaten galactic peace.
Meanwhile, Prime basically suggests that these bad boys are not only a highly organized military that had already taken over several worlds, have/had apparently several "home worlds", a "Science Team" that basically is as cruel and efficient as the Umbrella Corporation, and a "High Command" that remains nebulous regarding whether the leaders that we know about (ex. Mother, Ridley, Kraid, etc.) are a part of it, or a separate ruling body. In short, an organization that effectively established themselves as a threat to galactic peace long before the events of the original Metroid, and worthy of the spot of being the Federation's main rivals. (And for the sake of simplicity, we're just going to leave out the likes of the various other races that Prime introduced that
Again, these types of inconsistencies and others could all be explained away with Prime being the result of a split timeline of some sort, which is why I dig your bolded theory, too! And I don't think it would be all that confusing, as long as it's eventually clearly communicated (either through in-game lore, or recollections narrated perhaps by Samus, Sylux or some other party) that "things are different here". Audiences that saw Star Trek '09 got the gist that it and the soon established "Kelvin Timeline" was something different, and not just a reboot, pretty quickly, after all.