1. Taking over an AI's plane isn't coded in (offline mission-wise) and I don't think would be necessary. See #2.
2. A schedule for missions running would be needed for players to know when/where to take off with the mission. A multitude of mission choices for the staffer/CM would be needed for variety. Running missions in an automated loop wouldn't work if base captures are enabled. Don't want AI bombers attacking a friendly field after it changes hands. AI aircraft won't deviate from their plotted course/target, no matter who owns it at the time. A human staffer would be needed to choose which mission to run based on which field belongs to whom. Editing a mission's route to a new target is not hard if you know how to work the Editor. Would only take a couple minutes. Either that or have a nice selection of missions that are programmed for a variety of bases i.e. a mission made for each field of the map. I personally could do this in a day, possibly two, per terrain. The staffer would still be free to change the planeset/loadout at any time. That part is very easy.
3. I would do both. Just remember, with AI, only bombers can drop ord. No AI jabos. They will carry ord, but not drop it. Human pilots still could of course.
Great AI uses: bombers(from small to huge formations never seen before), fighters(escorting & intercept) or even just to furball. Just no AI jabos, except for immersion purposes of large flights, they just will keep their ord, even when fighting it out.