Things they should take out IMO
The Elite Four - Barring the 1st and 5th gen Elite Fours, I've hated the Elite Four. It serves no purpose other than saying you really beat the game. Whereas in the 5th gen they were a part of the story which I loved.
Gym Leaders - Unless Gamefreak gives the gym leaders an overhaul, this has become a tedious and boring part of the game. Again they only act as barriers and it has just become so lame to fight the in-game AI barring the Battle Subway - those fights can be fun.
You're kidding, right? Gym Leaders and the Elite 4 ARE the games. Why would they take out the game itself?