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According to GF,the timeline was pretty cut and dry, R/B/Y=R/S/E
~2 years later~
G/S/C
~LOR~
Pt
(NA)
B/W
~2.5yrs later~
BW2/XY
What I liked to do was replace the original games with the remakes, and the double games with the third version (meaning D/P didn't happen, but PT did) FR/LG and HG/SS didn't have a big difference in story, so those fit fine into the timeline.
However, with E.D we were made aware that there is an alternate dimension w/o Megas because the Kalos war never happened, so the Mega Stones and the KeyStones were never activated via Meteorites from the ultimate weapon.
With this, a brand new timeline can be created with Mega Pokemon. It can be inferred that each of the "Legendary" Trainers (Red, Gold etc) each have a Keystone *and* a Legendary Pokemon.
If Origins is indeed canon then we can easily create a timeline in the Megaverse, seeing as both Origins and ORAS have the same plot as the originals.
Red goes through his story in Kanto, meets Dr. Fuji and obtains a Keystone and Charizardite X and catches Mewtwo.
Brendan (confirmed male by Norman at the PWT) goes through his story, meets Steven who gives him a Mega Bangle, obtains Lati@s, gets Mega Stone for starter.
The other Trainers go through similar experiences and obtain a Key item.
The only differences are that Steven is champion in HG/SS, and Wallace is champion in BW2, but he stepped down in ORAS. Meaning Steven stepped down later in the first universe than in the Megaverse. The other difference is that the Battle Frontier is built much later in ORAS than in Emerald and there is already talk about the PWT, which shouldn't have been built until post-BW.
This leads me to believe that the events that take place in the Megaverse are placed differently on the timeline. Reds story has to take place at least 5 years before ORAS because Mega items are just being discovered and used by Trainers in his time while they are very well known by any above average Trainer in ORAS.
