In my opinion, making an all revamped system with individual stats for revenge damage rather than making a simple standard fixed revenge damage against flying units would be a mistake that wouldn't help balancing the system at all.
What I would like to see with flying units are 2 things :
-at the beggining of the game, it should not be invulnerable and be able to win the game on its own, that's why the revenge damage from infantry would help to complement archer damage in order to repel them
-at the mid and endgame, flying units should be able to do stuff, which they would never be able to do if revenge damage is increased because troops are stronger and more well equipped.
By mid game, the elemental damage from arrows do far enough more damage to flying units, no need to add any more penalties.
When suffering revenge damage, flying units should have no care of forged blades, and no care of whether it's attacking basic units or heroic units, it should not suffer more revenge damage than in the beggining of the game, otherwise flynig units will be garbish, and there I totally agree with Elendil's Cousin when he says that dragons should feel powerful.
If the revenge damage is a fixed standard damage, flying units will be especially good against fully-upgraded troops because it will not suffer more damage than if it attacked a basic unit, and then the feel of power will not be negated in then endgame.
Revenge damage should not destroy flying units, it should only work as a complement to archer damage at the begginning of the game, but it should not by any way get more powerful over time.
That is why if revenge damage is chosen to be implemented, I would advise a simple system with a fixed revenge damage if some conditions are fulfilled (infantry striked, maybe 4 or 5 men of a batallion at least, who don't cover in fear, and maybe revenge damage from heroes also).
The only interest of revenge damage is balance and helping flying units to resist more against archers though not being completely invulnerable from doing so.