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In FRLG You had to help fix a machine that allows Kanto to communicate/trade with Hoenn. That's the only connection I can think of that connects the timeline between the two games.
If I remember correctly, within X and Y, someone tells you that Mega Stones used to be regular evolutionary stones that were changed by Xerneas's power.
I'm pretty sure the circles have been there specifically to show you what kind of environmental effect your moves will have when using a move that changes with the environment.