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Here's how it goes.
Each individual cartridge is it's own Universe. However, the games follow a canon timeline of events that have already been confirmed via a Tweet by Toshinobu Matsumiya. Combine that with various in-game text by NPC's, this is how the Multiverse works.
Universe 1 - The events of RBGY happen, then three years later, the events of GSC happen. In between those two games, the existence of Dark and Steel Type Pokemon and Pokemon Breeding are discovered.
Universe 2 - The same events from the previous Universe happen in the same time span, however they are interpreted differently through FRLG and HGSS. At the same time, the events of RSE and DPPt take place alongside them respectively. After an undisclosed amount of time later, the events of BW happen, then two years later come the events of B2W2. Mega Evolution and Fairy Type don't exist, however Dark and Steel Type Pokemon have existed here since before the events of FRLG.
Universe 3 - The same events happen in the same time span as Universe 2, however they also have different interpretations; for example, ORAS is this Universes interpretation of RSE. All of the previous Regions do exist in this Universe, and so do Kalos and a currently unrevealed Region (which could be the Region Kalos was at war with). Mega Evolution and Fairy Type do exist in this Universe.
The dialogue between Prof. Sycamore, Sina, and Dexio can easily be explained. Sycamore studies Mega Evolution. He may just be uneducated that Mega Evolution exists outside of Kalos. Fairy Type Pokemon can be recently discovered and still have existed for several years. It could easily have been around since before the events of Kanto and still be considered a "recent discovery."
Cont.
