I don't really know if we'll be battling clones, exactly. In original games, they would change your over-world and trainer sprites to a random NPC every time we'd log online, so I suppose they'd likely do the same here?
What I believe would be even better is that, if they're not going to allow customization for May and Brendan, perhaps we could have a separate character for our online selves, which we would be able to freely personalize? Of course, since this isn't related to main story, there wouldn't be any clothing shop in-game. However, if they still wish to keep certain things blocked and have us unlock them, they could set certain requirements, such as battling X amount of time against a friend.