I do believe that levitation should become a condition... cal it however you like levitation flight, hovering.
The ability levitate should disappear and all pokémon that are clearly levitating or flying should get the levitate state, while flying pokémon that aren'tflying (looking at you dodrio) should not be considered flying or levitating.

More than this levitation should not grant immunity to ground type, but only towards some moves (earthquake etc.., while for example earth power or the new scorching sands can affect levitating pokemon). Fields should not affect levitating pokémon of course (but it is already like this).

Therefore aa Pokémon like magnezone or bronzong would be levitating by default. Also dustox, Giratina Origin form etc.. (yes many Pokémon, many ghost types).
Removing levitate could be a feature of many moves (for example flinching, paralysis etc.. could remove levitation or rock throw as well)

To me this would make sense.