I think it's important to remember that the story is meant to be beatable by 10 year olds, so I doubt they change the EXP Share mechanics or anything like that. If you want a real challenge, you'll have to look at post game stuff probably, which is why I'm dying for a battle frontier remake. If you want to make the story hard, it won't be too difficult as you can avoid using traded pokes, turn off the EXP share, and not use blatantly OP pokes like Mega Blaziken. Those moves alone will probably make it fair without ruining the experience like some challenges do for some people. I don't think difficulty will be a huge issue.