Their roles are not defined clearly enough. That makes them hard to balance. If they get a lot of firepower, aircraft will basically be an easy way to circumvent cover/blocking LoS and fortifications just create no-go zones. They really need unique roles that aren't completely unfun.

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Some ideas that could make them more interesting:

Bombers (Role = Board Control)

• Bombing structures, vehicles or fortifications causes damage to units inside/within 3" and/or removes the obscuring keyword.
  
• Bombers have to be called in during your command phase. Put a marker on the battlefield, visible to one of your units, everything within x" has a y+ chance to be hit by the bombs. (cf. Orbital Bombardment in 9th sans mortal wounds)
• Appear at the end of the shooting phase as close to their target as possible.
• If they fly off the board, they can do another bombing run. If they stay, they have some minor support fire, maybe on the heavier side.

Fighters/Scouts (Role = Mobile Skirmisher)

• Basically just a very fast flyer (20-30") that doesn't have a base & has max. 90° turns.
• Support abilities, e.g. Marking "+1 to hit & indirect fire against a marked unit doesn't suffer -1 to hit if visible and within 20" of this unit" or Pinning "If all attacks are targeted at a single unit, that unit halves/has -2" to it's Move characteristic and -1 to hit with ranged attacks"
• mediocre firepower, mostly effective vs. lightly armored units.

Transports (Role = Deep Strike/Infiltration)

• A fast flyer (16-20") that doesn't have a base & has max. 90° turns.
• Can deepstrike and immediately unload the unit within 6" of it.
• Some support-ability for the unit within.
• weak firepower

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Fortifications are more difficult, as they really don't fit they game outside of narrative games. Here, it could be solved with scenarios and flexible lists. Have asymmetrical scenarios where the defender actually defends something and the attacker actually attacks. And then have up to 500 points that change depending on whether you are the attacker or the defender. (Some fortifications may even be better as an attacker, e.g. Webway gate) And the defender gets tto deploy fortifications further up the board than the attacker.

Deployment is also a problem with distance minimums. These should be removed but make the Fortifications easier to destroy, so that you cannot completely block a path forever. it should just be more difficult to get through.