1. I'd add 2 kinds of battle: First, the 2D standard battle which would include one-on-one, two-on-two, and three-on three. And there would also be a 3D strategic action one-on-one mode. Every pokemon would have a stamina bar, determined by certain factors, recharging over time, or once they have been hit. Pokemon would be able to dodge attacks and charge to get closer or away with the stylus, lowering their stamina bar, making them rest when it's gone. Attacks and held items would still have effects, and attacks would still be similar, flame thrower would still be a stream of fire, but you could use the L and R buttons to turn, and use the stylus to move the stream of fire.
2. A ability to throughly interact with your pokemon, other than "You found another useless accessory on the ground, YAAY Arceus!" With flying pokemon, you'll actually able to fly everywhere above the map, and reach secret TMs and evolution item shops, and find rare flying types. You'll able to use ground types to go underground like P/D/PLA. And you can use water pokemon to use surf and dive like R/S/E and find sunkern ships and submarine with rare items.
3.There are no HMs, the trainer gets skills like cut and rock smash.
4.When you catch a wild pokemon, you can choose its ability.
5.A more developed storyline than " We want to capture your electric rat that is useless, and that our boss probably doesn't want anymore."
6.We get more regions, less version exclusive pokemon, and less event legendaries.
2. A ability to throughly interact with your pokemon, other than "You found another useless accessory on the ground, YAAY Arceus!" With flying pokemon, you'll actually able to fly everywhere above the map, and reach secret TMs and evolution item shops, and find rare flying types. You'll able to use ground types to go underground like P/D/PLA. And you can use water pokemon to use surf and dive like R/S/E and find sunkern ships and submarine with rare items.
3.There are no HMs, the trainer gets skills like cut and rock smash.
4.When you catch a wild pokemon, you can choose its ability.
5.A more developed storyline than " We want to capture your electric rat that is useless, and that our boss probably doesn't want anymore."
6.We get more regions, less version exclusive pokemon, and less event legendaries.