1. While there are targets that are just to well defended to risk aircraft against, these targets represent <1% of the targets that need to be serviced. Most of these 'lesser' targets are also mobile making targeting by long range missiles difficult, sometimes impossible. It is cheaper, and frequently more effective, to use aircraft to engage the majority of these 'lesser' targets than long range missiles. Examples would be the Iraqi Army in Kuwait and the SCUD missiles in western Iraq during Desert Storm.
2. The use of an aircraft as a '1st stage' for air launched missiles can produce equal or better performance to their larger ground launched cousins while allowing the launch aircraft to stay out of the engagement range of fixed defenses around high value targets.
3. Aircraft are more flexible. Aircraft can form a strike package with attached tankers and electronic warfare assets can penetrate most defenses, fake such an attack to distract an enemy, or displace over long distance to strike from an unexpected direction. Missiles cannot do this.
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