in the mega episode III marin and alain part ways and marin returns to kalos. alain is an unwitting pawn of lysandre and stays in hoenn. I know they're not seperate continuties, because ash is mentoined in the mega episode. so maybe marin joins ash and the gang and ash meets alain in the confrontation with team flare.
There is no way to know, however, I don't think so. Pokemon usually never cross timelines with the anime and the anime specials, so as not to confuse the watcher if they haven't seen the Mega Evolution specials. I'm sure it's a possibility.