She actually seems to confirm that idea later in the Episode as she mentions that there is a universe where Mega Evolution isn't discovered and the war in Kalos never happens, more then likely referring to the previous games as they never had Mega Evolutions in them. So there should be at least two timelines, the first being the one we're more familiar with (FRLG/RSE>HGSS/DPPt>BW>B2W2), and the second being the new one where Mega Evolution is present (ORAS>XY).
Overall, I'm a bit mixed on the idea, but depending on how they handle it, it could lead to some interesting developments. Especially when it comes to the likely DP and BW remakes as now they can take more liberties with them.
Pokemon:
Generations of Future Past
Starring Hugh Jackman as Pikachu
Generations of Future Past
Starring Hugh Jackman as Pikachu
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