Well how deeply do we probe this? Why does it stop being "your game" when the narrative shifts to another universe, but not when it shifts simply to another person? If we look at it logically, the main character of your Pearl Version cannot possibly be the same person as the main character of your SoulSilver Version. But you gloss over that in order to maintain the pretense that it is *your* single, contiguous journey. Nevertheless, they are an entirely different person in and entirely different place... which is really just what the XY and ORAS protagonists are as well. The only difference being that the "entirely different place" in question is shifted over by one dimension.I mean, I like the idea of all the Pokemon games being my personal journey (granted, it becomes a bit funny when I've beaten two different versions of Team Aqua twice, but hey ho). Having Pearl/SoulSilver/Black etc. being 'non-canon' in a way in these new games feels... off to me. Yeah, those events still happened, but it's no longer my game anymore.
Saying that the old games are now "non-canon" is incorrect. In fact it is quite the contrary. Without the multiverse plot point, ORAS would most likely have just overwritten RSE and rendered them non-canonical, just as FRLG did to RGB and just as HGSS did to GSC. The multiverse plot point circumvents that and introduces a way to continue making remakes without eliminating the originals from the canon; in fact, it adopts those games into its own mythos. Instead of ORAS *replacing* RSE and making it so that they never happened, we now know that RSE very much *did* happen (as well as the previously overwritten RGB and GSC games if one extends the plot point to its natural conclusion), just in another universe.
It is a "throwaway line," if the entire motivation for a character's opposition to a proposed solution and desire to find an alternative can be considered a "throwaway line." That would be like having a movie where somebody proposes to deal with a viral outbreak by burning the entire city that it is spreading in to the ground, and then when the other characters try to explain why that would be horrible, saying that their arguments are just "throwaways."Then again, it's a throwaway line from Zinnia, whose character is such that she might not be 100% accurate anyway, so I just chose to disregard it for my personal canon. Nothing stopping fans who do like the idea using it, but I personally don't. If it ever progresses past that brief mention, though... I might just think that Pokemon has jumped the shark a bit. Sorry.
Moreover, it's not just Zinnia who says that the alternate world exists. She states that this is something that has been observed by the Draconids for generations, through the distortions in the world created by Mega Evolution. It's existence has been documented for a long time.
And, if this is them "jumping the shark," then lay that blame on BW. Those games introduced the concept of multiverses and alternative timelines into Pokémon. *If* the Gen IV games didn't already do that by talking about such things in the PokéDex entries for Porygon-Z and Palkia. All that ORAS did was put the idea a bit more into the limelight and expand on it. And frankly, even then, I don't see how this could really be considered all that "shark-jumping." It's not really that revolutionary. Alternative timelines and universes are fairly common ideas even in non-science fiction media, and I know that I and many others already assumed them to apply within the realm of Pokémon because the games, with their dual-version structure, seemed to lend themselves so naturally to the idea. If anything, I think that it at least pales in comparison to the over-the-topness of Platinum's stoic nihilist villain who wanted to destroy the entire universe and remake it in his image just because he hated the idea of souls, or RSE' villains who wanted to help Pokémon... by destroying an environment that many kinds of Pokémon inhabit.