I can imagine a considerable problem with the command structure is that if you've got a war that forces are badly prepared for and reluctant to fight in, you have to tread much more carefully with the orders you give your small number of highly trained (and relatively smart) pilots based on home soil than your large number of dispensible conscript troops you've driven into the conflict (or your gung ho special forces). Easier for them to disobey, and much more cause for alarm if they do, and no matter how dedicated they are to following orders, there are fewer pilots and planes to risk than armoured personnel carriers, artillery units and dated tanks.