I think the storyline will be your general pokemon storyline. You're a kid coming of poke-age seeking to be a master and some evil team, gets in the way. I think that's a given.
But outside of that there are things that I hope they do differently. Like maybe more side quests that can be done, that have an actual impact on the game ... not just 'Find where I am hiding in this room and I'll give you an item' Something more like, 'My slowbro is getting eaten by a snorlax ... help meeeeee.' And, I dunno, if you oblige to take the quest, people from different towns say stuff like 'oh you're that guy that blah blah blah' and maybe get a ribbon/special pokemon from it. You know? . Like they did with the farfetch'd thing in GSC. Little chance of that happening, but it's something that I'd like haha.
I'd also like to see stuff like optional gyms and stuff - again effecting the storyline, getting recognised as a stronger trainer as you complete more optional challenges.
I think there will be more towns and what not, so they can show off the fancy 3D thing and milk it for all it's worth. And that in itself gives me high hopes for there being more than 8 gyms.
The only difference I can see in the story as opposed to the other story lines is maybe Zoroark is the evil 'team' and instead of hunting down Giovani etc etc you actually have to try and stop Zoroark from destroying the place. But I suppose if they were going to milk the poste-rmon in a storyline in-game they would have already done that with Lucario...
I mean this is all wishful thinking, but as far as the story line goes I doubt we'll see any more than we have already seen from previous generations.
I believe that is more than two sentences .