Uhhh....yeah, being able to control ur poke while flying (or having an animation where u see ur character flying on the poke through the region)
Different types of starters (never gonna happen, is it?)
Instead of having roaming pokemon, you hop on ur bird poke and chase them (or for like Suicune, chase them on a surfing poke), until they get tired/angry, then battle them.
Just a team like team rocket, not too major to the plot.
No new legendaries!!!
2 full regions in a game. all is impossible, even all ones from the handheld main series, but two full ones should be good.