...Okay, I must have misunderstood something.
And I say that FR/LG are in the same time period as RBY (or rather, remakes of them with advanced graphics and the Sevii Islands added in) because of the Legendaries' availability. What I understood about the Legendaries missing from GSC (I think I read this in the official strategy guide or something, I don't exactly remember. But it WAS from a Nintendo source) was that they were missing because the R/B character had already caught them all, and them being in GSC would ruin the idea of the Legendaries being one-of-a-kind, which is why I used Mewtwo as an example (after all, as we all know, Mewtwo IS one-of-a-kind in the timeline). However, they show up again in FR/LG, obviously, which tells me that they are the same games as RBY, just redone. Therefore, as I mentioned before, it is most likely that R/B never existed as far as the timeline is now concerned as FR/LG take their place. As far as Yellow goes, though, I'm starting to consider that not canon partly due to the lack of a remake and partly due to how it was sort of a rewrite that's been overwritten (adding your partner Pikachu into the story, then dropping it with FR/LG). There's also the fact that it was labeled "Special Pikachu Edition", which kind of leans toward the idea that it was just a special thing for kids to get to play as if they were Ash, Pikachu and all.
I hope that made sense.