timing of missions is one problem. players don't want to wait for a mission to start. and this is quite obcious when there are only 5 missions per day. this could be easily solved if there was a missions starting every 5 minutes. at an average length of 30 minutes per missions that would mean there are always 6 missions available.
but the more important point ihmo is that missions are not flexible enough. imagin there's a mission with b17s, p51s escort and p38 jabo. but you prefer lancasters, spitfires and p47s.
there should be a much simpler version of the mission builder, something like a pilots-for-a flight-collector. a few lines of text for mission objectives and a take-off (and target) field. if you decide "i'll go heavy to field X", a quick glance at the list of this missions will reveal if someone else is also going to do this, and you can roll together. also, this list gives a hit what might be needed in an attack, or if there are enough defenders at a field.
maybe this doesn't even have to be some kind of mission editor (e.g. multiple players on the same mission), but just a player-info feature where every player can note down what he (or she) is doing, and more important, going to do next (again with takeoff and target field, and sortable by this). It would then be possible to fly together with those that are planing to do the same before even waiting in the tower. that would also solve the timing problem.
a big advantage of missions vs. completely uncoordinated effort is that everything is there that is needed (unless the creator of the mission forgot something). in MA play usually noone knows what really is needed somewhere. because noone knows what everybody is doing, not even those that are working on the same objective. if there was a pop-up box at the start of every flight, asking "what are you going to do?", and a dot-command (".next ") to set future plans, this would probably help to syncronize the take off times of players flying from the same fields to the same targets.
