salamence never needed wings to fly. have you ever seen in any of the media salamence needing to flap its wings to fly or stay afloat? bagon always had the ability of flight, it just needed to grow older and realize it had latent potential.
think about it, its wings are small and thin in comparison to how large and bulky salamence is. its megaevolution is salamence giving up the pretense of its ability of flight is due to its wings, and deciding to turn something vestigial into a powerful weapon.
