I always wanted a 3D pokémon game would be just like gameboy version...
Walking, encountering wild, roaming pokémon... some NPC trainers to battle with, but also able to interact with other online players via mic. typing would just be less attractive IMO.
Also should be able to use the Wiimote freely; throwing the ball with the wiimote is just one of many possibilities. Maybe Choosing the pokémon you want to battle with, from the left/right side of the screen, or just play with one of your pokémon thats out of the ball... more you play with them, the more they grow to like you and... "fill in the blanks"
The map should be huge, to see higher levels of pokémon, you should just travel, maybe with a bike like the other games, which also could be interactive with the wiimote and nunchuck.
If I am able to come up with this idea, I'm sure there is someone working at Nintendo to do too... but if there isn't, I should copyright this sh*t.
