I would like different difficulty levels from the start, the whole map available from the start and the AI to determine the opponents/wild Pokemons levels!!! All 3 ideas go together as well.
If the AI determines the level of the opponents/wild Pokemon then you could travel anywhere in the map and start at any gym with no problem. On the higher difficulty levels, gym leaders could always be 5-10 levels higher than you to make it more of a challenge. The story could be made to have several sub-stories that all center around the final gym which could be the peak of the main story.
After having the PWT in B2W2 I would love to see a top 16 tournament after you collect the badges and once you win it, you get to battle the elite four and champion!
A few other things that I'm sure have been mentioned in the previous 166 pages are
- two save files
- Pokemon follow you
- Choice to make HM's as special abilities only and not a move