I guess the best way to implement this would be to allow formation of aircraft groups. If one aircraft is in flight, a second aircraft can target the first. Once they meet, the player is asked if the second craft is supposed to join the first craft in a group. After that, the group can be given orders as a single "unit" (one of those orders being "disband group").
This would also simplify multi-craft air battles.
It should also be possible to send the craft out in groups when launching from a base.
Oh, and of course, we would need to think about the behavior of mixed craft groups: if a group made up of an interceptor and a skyranger reaches a crash site, is the group automatically disbanded (because the interceptor can't perform ground missions)?
We should also implement a mechanic that allows transport craft to hover over ground mission sites instead of immediately landing, to allow other transport craft to catch up...
There's a lot of stuff that needs tweaking and changing and adding for this to work (I still like the idea, though - but it needs some balancing, I think)