The mission planner right now... doesn't do a whole lot. You might as well say 'take off from 64 and head to 72!' My wish list of ideas:
(Note: I don't use mission planner much so some of these may already be there. Also... some of these are a bit 'out there' I am just thinking out loud)
The ability to set waypoints with altitude, with time each waypoint should be reached calculated by plane speed. This would allow for coordinated attacks from multiple directions with precision timing.
The ability to designate flight leads
Instead of grouping by plane, group by flights which can have different types of planes
The ability to designate targets by flight or even down to each plane... i.e. which hanger on a field each plane should hit. Pop up of target would appear where you could pick object.
The ability to type in notes for each flight
The ability to set mission channel (Vox and text) in the mission planner and have them auto-tune when the mission starts.
The ability to have different take of times for each flight.
The ability to have flights from different airfields
The ability to include GV in mission planner
The ability to join a mission while you are in-flight with another plane (that plane would auto-land to nearest airfield)
Others?