I don't know why but flyers seem more like skimers than flyers to me. So here is a proposal to difrent types of flyers and adjustments to flyers.
First thing is reduce the amount of hits a Flyer takes from ground fire when moving and add in anti air units. Anti-air units can hit Flyers without the range penalty.
New Anti Air Units.
Imperial Guard. Hydra (mounted on chimera chasis) and Hydra Turret. Decreas Maurader ability to attack Air units makeing it more of a bomber/ground attack fighter.
Hyperious tarantula turrets (less armor than bolter turrets), and Hyperious Missles Upgrade to give Wirlwinds AA mounts.
Fire Storm Grav Tank, Also night wing acts as an AA/Interceptor and suffers no range penalty.
Flak Wagon and upgrade Waagh Banners with FlakGunz research at pile of gunz.
Chaos Space Marines.
Hell Talon acts as AA/Interceptor unit. (Reduce Ground Attack)
Upgrade SkyRay missle Launcher with Anti Air Missles. Add Sensor Towers which allows the nearest Listening Post to fire Hunter Killer Missles at any air craft in area.
Necron Guass turets and Towers act as AA mounts. Necron Monolith acts as an AA and Necron Lords/C'tan are imune to air atacks.
Increase Raven firepower as an AA/Inteceptor unit.
Sisters of Battle
Increase Lightning firepower to act as AA mount.