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Consider the following:
Step One:
>Give all flying Pokemon 2 base animations: One flying animation and one grounded animation.
Example: Xatu now has its current gliding animation, and a new standing animation (like its old sprites), that it uses when using roost, or after "smack down/gravity".
Step Two:
>The Flying-type loses its immunity to ground types moves. Levitate is no-longer an ability.
Step Three:
>Ground types moves now, be default, MISS if the target pokemon is not grounded.
Example: If a flying pokemon is using its grounded animation, the move succeeds. If the pokemon is clearly off the ground (Haunter, Magnemite, flying birds and bugs), the move misses.