Pokemon following you around like in Yellow,HG,SS - I'd like it, but I doubt it would be implemented again anytime soon
Berry Trees Back - I'd like it I suppose, to allow us to continually have berries.
New Battle system (6 on 6, etc.) - 3v3 is enough, and having any higher than that would be very silly.
Multiple Regions - One region is enough, and plus, the game cards don't have enough space for two "full" regions I believe.
Battle Frontier return - I wouldn't play it much even if it returned, although I might play Battle Factory some, but otherwise, I'd be okay either way.
New Starter types - No. Just no. Fire-Water-Grass is fine, and it's a staple of Pokemon.
Dark type Gym Leader - It'd be nice, but what gym number would it be?
Tournament instead of elite four - No, yet again. The E4 setup is good, and I'd hate tournaments.
Return of team rocket - I wouldn't like this one at all if Team Rocket returned.
New Eeveelutions - It'd be okay, but having a Dragon one would be to "over-powered" so I don't think they'll have one for Dragon.
New storyline(Not the old ten year old sets out to be champ and stop bad guys) - It'd be okay, but I still kind of like the obligatory plot line that has been in the games since the 1st generation.