I suppose that removing shadows (or shifting shadows away from the character) would help. Also, there are different render layers. If not specified, "lower-object" will be used. I guess setting it to "air-object" could help.
(EDIT: There is another mod that specializes in flying characters: Jetpack! Looks like I've been on the correct track, because in prototypes/phase3/jetpack.lua, lines 174ff. of version 0.3.11, Earendel makes flying versions of all characters where he does remove shadows animations and changes the renderlayer to air-object. Additionally, he removes footstep_particle_triggers.)
By the way, setting the shadow animations to nil won't work! Shadow and no-shadow animations must have the same count of directions and frames. Replacing the images with a transparent image should work, though.