Hi,
I would like to suggest adding some distinct features to mounts that would be able to fly in later official expansions (examples: Gryphon and drake).
Ideas:
water walking - the mount hovers over water at regular speed instead of swimming (unless you force it to dive maybe?)
Reduced fall damage - the mount plays fly animation while falling. Fall damage reduced by 50%.
Whether these or other ideas were implemented, it could come with a new "Expert mount training" for a heavy price.
An alternative to this expert mount training would be to balance these mounts out by setting their speed at 90% or 95% instead of 100% so the regular epic mounts had a small speed advance while the flying mounts had the maneuverability advantage.
Conclusion: These ideas are just a brainstorm to make sense of the flying mounts being in the game while keeping them grounded to prevent breaking the feel and balance of the game.