The problem is that flying armies can hide on mountains and water. Until such time as the game allows ground units to attack flyers on such terrain there is no incentive to have strong ground based armies because so many maps allow flying stacks to hop around without being attacked. This allows you to bypass the front lines and reach interior cities that strong ground units can't.
Wizards are already great at countering all the flying armies. They just cost a lot. Elves are nice too but they also cost too much. If the cost of those units was reduced to say 750 and 225 we'd see a LOT more Wizards and Elves and thus a lot fewer flying units and therefore more ground units. Eagles used to be fantastic at chasing down flying units until players complained they were too good and then they got weakened so that now all they are good for is killing Pegasi/Gryphons/Crows. If the Eagles anti-air power was restored this would be another incentive to use more ground based units.
Stack anti-air is available in 2 items. I think one of the new heroes has it as an ability as well. It's not common but it does exist. If Wizards/Elves/Eagles were changed I think these 2 items and the new hero would be enough to keep flying units more in balance.
follow rock-scissor-papers patterns
In the interest of fantasy theme I prefer to call this Iron Golem-Rust Monster-Mind Flayer
KGB