I'm coming to this discussion rather late and haven't had a chance to read all the previous discussions so I'm sure many of you have already addressed some of these issues.
Complexity - By the book, the rules are far more complex than needed and don't really give you much benefit. I ended up creating a Visio flow chart to assist with how to deal with various scenarios. The complexity comes from inconsistency. +4 to hit with a strafing run, +2 for bombing, control roll for range in A2A combat, etc. Consistency cures complexity in most cases.
Order of Operation - The rules are ambiguous in regards to if you move air or ground first. I recommend making it standard that air moves first and completes all air activities before moving to the battlefield. This removes units from the initiative count.
TMM - Someone else suggested this and I agree wholeheartedly. Aerospace units should get a TMM consistent with ground units. And the TMM can be used for your control rolls.
Air Movement - Too predictable and, as mentioned, there's little reason to bring units with a 9a movement. I moved to using one classic battletech hex map to represent movement and gave all units an elevation. One elevation is equal to 1 hex of movement for consistency. Elevation can be from 1 (battlefield attack) to 12 (upper atmosphere). 1 hex costs 1 Movement. Turn 1 hex face for free and lower elevation by 1 for free per hex of movement. The battlefield is represented by a hex in the center of the map.
Control Rolls/Tailing - I get what you're trying to do, but it is unnecessarily complex in practice - particularly if you have 4 v 4 air battles. I solved this by making a control roll during the attack phase. The high roll determines the range. Declare target. Control roll. Victor declares range. Roll attack. This eliminates the need to remember who had advantage on whom, etc.
Ground Movement - Allow the pilot to declare an elevation so they can determine the range to the target. This solves the problem of all attacks to the aerospace fighters having the same To Hit Number. Range can be measured to the closest point to the flight path or elevation, whichever is higher. Elevation can be up to 24" for those high-altitude bombing runs.
Ground Attack - Using elevation eliminates the need for special modifiers between the different attacks. Maybe you keep the modifier for the strafing run vs. a strike since units with ENE can do full damage. Otherwise, use the elevation/range.
Anyway, hope this helps.