- Slight sprite differences between male and female pokemon (which will increase the likelyhood of wanting to catch a male and female of each type)
- Trainer customization
- The option to see your Pokemon walking with you on the world map
- A different perspective in battles: Side view or 3/4 view (Final Fantasy Tactics, etc.)
- A way to defend your championship when you become the Pokemon champion
- The return of the secret base, day/night system, and time-specific events
- Character speech (especially for the Pokemon. I'd love to hear Pikachu say his name like on the show!)
- Ability to travel in a party with other trainers (especially fun for 2-on-2 battles)
- Stylus-controlled fishing
- The ability to delete HMs without having to go to a specific guy to do it...
- The anime Team Rocket as enemies who will occasionally swipe one of your pokemon, prompting a side mission to rescue it.
- The ability to name your Pokemon and call it out with the Microphone
That's all I can think of for now...