Psst, ZLS, the price already dropped. It's been dropped for about a week now. =P
Well, that's the way it was in the originals... And I believe some of the gyms even got a level boost! The Gym Rebattles are annoying, I'll give you that... However, it was the same way in Emerald, more or less.

Platinum-style battles would be interesting; but I don't think it should be restricted to randomly maybe having 4 Leaders... It should have a maximum of something, but a static max. And maybe being able to fight them over and over on the same day, like HGSS allowed.
A better Subway system would be nice; but the only thing that they haven't done for that is add in Frontier features; and that's better off on it's own.
A Kyurem Storyline is all but confirmed for Grey; and
that's not even confirmed yet. xD
Keldeo having a Side Story... Only way I see that happening is if there's a ticket that requires you to have all three Musketeers; since it's an event Pokemon... Much as it'd be awesome. =/
Abyssal Ruins should definitely be explained; but... Well, side areas like that haven't been explained much; look at the Regi areas in RSE or the Stone Tower in D/P/P... =/