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The order in which the player chooses the characters in each scenario doesn't change the story. It only shows sides of the story, and some scenarios come into contact with others IE Ven and Aqua's meeting at Enchanted Dominion. You can learn more via the BBS sticky in this section.
I think it will be like the Sonic Adventure Battle Game from back in the day, basically it will just ask you if who you would like to be, than after completing one you can play another, pretty much restarting the the game, but getting new additions to the story, filling in gaps, from the first story you played.