That's a very shaky argument; at the time of Diamond and Pearl's release, there was no indication that Johto would be remade so that it could have access to the newer pokémon, of which there were nearly twice as many as there were in GSC. There wasn't really even a hint that remakes would be a trend - when Ruby and Sapphire were first released, they were completely and totally isolated, and scores of older pokémon were unavailable in any legitimate way. Emerald only added a very small fraction of what was missing, and without FRLG, Colosseum and XD would be needed to get most of the rest. The release of FRLG just felt like a natural fix to the situation at the time, especially with Colosseum covering most of the Johto pokémon. Diamond and Pearl, on the other hand, had every non-starter and non-legendary bar Tangela and Tropius between the two of them, and even then, they still had the Pal Park for the missing numbers. So when DP's very first major plot point was predicated on the Red Gyarados sighting at the Lake of Rage, there was nothing to indicate that HGSS would ever exist, only that Diamond and Pearl, and later Platinum, ran roughly concurrent with GSC in the timeline.
Game Freak isn't overt in their chronology, and they're typically very subtle about it, but it's there. Each set of games has an isolated story for the most part, but there are brief little instances and details that bring all of the games together - things like Red's appearance on Mt. Silver and later at the PWT, or the aforementioned Lake of Rage incident, or references to AZ in ORAS. The very fact that the strange souvineer exists in the first place, and that it's found in Kalos a generation before its supposed home region is introduced almost certainly means something. So to assume that SM must take place after XY is fallacy, because there's nothing to say that SM doesn't hold a chronological precedent at this point either, irregardless of the veracity of the leak.
Game Freak will do what Game Freak wants in regards to the overall layout of the storylines, and the way the games fit together. They're the people who took something as innocuous as Steven Stone's hobby, and turned it into a major game mechanic that was a viable plot point ten years later for a region that's supposed to be wholly unrelated to Hoenn, except for the fact that AZ appeared there once in a while during his thousand years of wandering. They've already established a precident of jumping the timeline, and there's no reason whatsoever to say that they'll never do so again.
Frankly, while I'm taking these leaks with a large grain of salt, the standard "Collect Eight Badges - Defeat Evil Team - Conquer Elite Four" formula that all of the main series games have used has become quite stale. With the confirmation that Masuda has stepped from the role of director to that of producer for these games, I don't think anything relating to storyline formulas is going to be rock solid, and I would like to see a shake-up in the formula to revitalize the standard playing experience.
Also, before I forget, if these starter leaks are indeed true, I would like to formally make the jump from Team Litten to Team Popplio.