The ACU shooting at Aircraft Problem:
All aircraft, excluding air transports and experimental air units, have large, spherical hit-boxes that are actually bigger that the aircraft is. In vanilla Supcom they had square hit boxes that reflected their actual size. This was changed in Forged Alliance to make anti aircraft guns, which at the time were widely decried as useless and inaccurate, more effective. All aircraft now have hit boxes 1.6 unit diameters, except for strategic bombers and T3 gunships, which have diameters of 2.
(This is why non air transport aircrafts cannot have personal shields, because those wrap around the unit model, which is square and significantly smaller than their spherical hit boxes)
Due to this change aircraft became very easy to hit. You can see for yourself as in games aa guns rarely miss most aircraft, excluding spy planes and other fast units. In the case of some units, like the air scout, their hit boxes were increase by a factor of 9.
Before the change in aircraft mechanics (increasing all aircraft hit points by a factor of about 10, and increasing the size of their hit boxes) allowing the commander to shoot aircraft would have been fine. Due to the low muzzle velocity on most direct fire units and the aircraft's previously tiny hitboxes, direct fire units would have rarely ever shot down aircraft because their weapons could never hope to track them. The reason they were never allowed to shoot aircraft is because you would see mavors and battleships blasting away at air scouts due to a lack of targeting priorities.
This priority problem could easily fixed by telling direct fire units to prioritize land targets over air targets. Sadly, however, the new and gigantic hit boxes on aircraft made this undoable, as land units could now easily target and blow air scouts out of the sky by simply pointing in their general direction and firing.
If one wanted to make weapons in Supcom realistic, one would have to give units appropriate target priorities and eliminate the SizeSphere stat on aircraft. To compensate for the reduced effectiveness of aa, they should be given higher muzzle velocities comparable to interceptor weapon projectiles, which travel at 120 units per second.
This would eliminate the weird effect when aa projectiles appear to miss aircraft completely, but still impact their hit boxes and do damage. At the same time it rectifies the inaccuracy on aa guns and allows ground units to fire at aircraft.
If aircraft hit points were reduced by a factor of ten to make them lighter and more realistic, and also reducing aa weapon damage by a factor of ten, you could then allow interceptors and aa guns strafe ground units with their comparatively light weapons while light assault bots and other units return heavier but less accurate fire. It would also would eliminate those awkward moments when your tank column spends a whole minute trying to destroy a parked interceptor which has more hit points than any of them. LOL
This would not change the ground v. air balance significantly, but it would make supcom look so much cooler.
If I had time, I would release a mod for this. If anyone else wants to, feel free to do so.
P.S. You may be thinking, "Wait! Reducing aa damage and hit points by a factor of ten would cause weapons to deal decimal damage and make some aircraft have decimal hit points! You would have to change the air balance completely to eliminate this!".
Fear not. The supcom engine can handle decimal hit points and damage. For example, the UEF riptide does 13.5 damage per shot. A unit with 14 hit points would have 0.5 hit points left after being shot once by a riptide and still survive. Although fractions of hit points are not displayed (meaning 0.5 hit points would not be displayed as such), they are accounted for in the engine and therefore would not cause any problems.