I too play as UAV ops a lot and find that most of my time spent manually flying is trying to dodge fire from the enemy aircraft. Something that annoys me, though it might not be patchable because Arma, is that the CAS aircraft spend a lot, perhaps too much time attacking friendly aircraft.
Coordination between UAV operations and, well, everyone seems to be lacking in general, but that's the nature of the role; it's not "necessary" to complete objectives, and nobody seems to feel the need to call for support.