>>22081675FUCKING THIS
Why is it so hard for you guys to understand?
3000 Years Ago, Ultimate Weapon, Faries, Mega's, blah blah blah -> OR/AS + FR/LG/Origins -> Pt. HG/SS -> B/W -> B2/W2/X/Y
Mega's existed in Hoenn, but were kept mostly secret by the Sootopolians, and weren't fully researched until years later in the Kalos Region, which saw their own share of Mega's in their history.
Zinnia was crazy, and we don't know for sure that what she was saying was even true. However, we know from NPC's in Gen 5 that alternate universes are canon, and Aqua/Magma on the docks in OP's pic speculate this also, so lets ASSUME Zinnia is right. All it is, is a clever reference to R/S/E. Those games are now considered non-canon in the main timeline, but still exist in their own "no mega's" timeline which Zinnia refers to.
That's it. There's no DEEPAH LOOOORE with mystery dungeon, or R/G/B/Y, no time travel, no Zelda timeline.
Just one simple timeline, with a reference to an older, non-canon game, being the setting of another universe without mega's.
It was supposed to be a reference, simple fanservice, and retards looked way to far into it, trying to justify theories of why there a 2, 3 even 4 fucking timelines in Pokemon.